diff --git a/404.html b/404.html index e054075d..cd6c0f53 100644 --- a/404.html +++ b/404.html @@ -18,8 +18,6 @@ - -

Page not found (404)

- Content not found. Please use links in the navbar. -
- -
- - -
- - - - - - diff --git a/CONDUCT.html b/CONDUCT.html index 591a58fd..98148e7f 100644 --- a/CONDUCT.html +++ b/CONDUCT.html @@ -3,8 +3,6 @@ - -
- - -

Contributor Code of Conduct

-
-

As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.

We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.

Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.

@@ -77,31 +67,17 @@

Contributor Code of Conduct

Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.

This Code of Conduct is adapted from the Contributor Covenant, version 1.0.0, available from http://contributor-covenant.org/version/1/0/0/

-
- -
- - - - - - - - - diff --git a/articles/index.html b/articles/index.html index 6baaa238..ae691734 100644 --- a/articles/index.html +++ b/articles/index.html @@ -3,8 +3,6 @@ - -
- - -

Articles

-

All vignettes

-
MSnbase: MS data processing, visualisation and quantification
MSnbase IO capabilities
@@ -85,22 +75,12 @@

All vignettes

- - - - - - - - diff --git a/articles/v01-MSnbase-demo.html b/articles/v01-MSnbase-demo.html index 29cbd556..a1420077 100644 --- a/articles/v01-MSnbase-demo.html +++ b/articles/v01-MSnbase-demo.html @@ -19,8 +19,6 @@ - -
@@ -98,15 +90,10 @@

Johannes Rainer

Sebastian Gibb

- - - Source: vignettes/v01-MSnbase-demo.Rmd + Source: vignettes/v01-MSnbase-demo.Rmd -
- - -
+

Abstract

This vignette describes the functionality implemented in the MSnbase package. MSnbase aims at (1) @@ -118,8 +105,7 @@

Sebastian the Bioconductor (Gentleman et al. 2004) project.

- - - -
- - -

Authors and Citation

- -

  • Laurent Gatto. Author, maintainer.

  • -

    Guangchuang Yu. Contributor. +

    Guangchuang Yu. Contributor.

  • -

    Samuel Wieczorek. Contributor. +

    Samuel Wieczorek. Contributor.

  • -

    Vasile-Cosmin Lazar. Contributor. +

    Vasile-Cosmin Lazar. Contributor.

  • -

    Vladislav Petyuk. Contributor. +

    Vladislav Petyuk. Contributor.

  • -

    Thomas Naake. Contributor. +

    Thomas Naake. Contributor.

  • -

    Richie Cotton. Contributor. +

    Richie Cotton. Contributor.

  • -

    Steffen Neumann. Contributor. +

    Steffen Neumann. Contributor.

  • -

    Arne Smits. Contributor. +

    Arne Smits. Contributor.

  • -

    Martina Fischer. Contributor. +

    Martina Fischer. Contributor.

  • -

    Adriaan Sticker. Contributor. +

    Adriaan Sticker. Contributor.

  • -

    Ludger Goeminne. Contributor. +

    Ludger Goeminne. Contributor.

  • -

    Lieven Clement. Contributor. +

    Lieven Clement. Contributor.

  • -

    Sigurdur Smarason. Contributor. +

    Sigurdur Smarason. Contributor.

  • -

    Miguel Cosenza-Contreras. Contributor. +

    Miguel Cosenza-Contreras. Contributor.

  • @@ -149,8 +139,6 @@

    Citation

    Source: inst/CITATION
- -

Laurent Gatto and Kathryn S. Lilley. MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Bioinformatics 28, 288-289 (2012).

@Article{,
   title = {MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation},
@@ -167,27 +155,14 @@ 
Citation

   journal = {bioRxiv},
   year = {2020},
 }
-
-
- - -

Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

-

Site built with pkgdown 2.0.9.9000.

-
- - - - - - diff --git a/index.html b/index.html index b14f3df4..7e5a6517 100644 --- a/index.html +++ b/index.html @@ -19,8 +19,6 @@ - -
-

The MSnbase package

@@ -138,9 +129,7 @@

ContributingContributor Code of Conduct. By participating in this project you agree to abide by its terms.

-
-
- -

Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

-

Site built with pkgdown 2.0.9.9000.

-
- - - - - - diff --git a/news/index.html b/news/index.html index 1edbcb2c..1236c08b 100644 --- a/news/index.html +++ b/news/index.html @@ -3,8 +3,6 @@ - -
- - -

Changelog

Source: NEWS.md
-

MSnbase 2.31

@@ -76,11 +67,11 @@

MSnbase 2.31.1chromatogram() method.
  • Fix Rd notes.

    • -
    -

    MSnbase 2.31.0

    +
    +
    +

    MSnbase 2.31.0

    • New Bioconductor devel.
    -

    MSnbase 2.29

    @@ -2258,28 +2249,16 @@

    Changes in version 0.1.0

    - -
    - -
    - - - - - - diff --git a/pkgdown.yml b/pkgdown.yml index 2b7efa8a..8a28b3fb 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,11 +1,11 @@ -pandoc: 3.1.1 +pandoc: 3.1.13 pkgdown: 2.0.9.9000 -pkgdown_sha: 9a6bbfc6ecf3aaf94406783beb0154fec0f3e87c +pkgdown_sha: cf719ba763fdaaf9b285cb2871dad8c746e9e6b7 articles: v01-MSnbase-demo: v01-MSnbase-demo.html v02-MSnbase-io: v02-MSnbase-io.html v03-MSnbase-centroiding: v03-MSnbase-centroiding.html v04-benchmarking: v04-benchmarking.html v05-MSnbase-development: v05-MSnbase-development.html -last_built: 2024-05-01T08:21Z +last_built: 2024-05-15T16:28Z diff --git a/reference/Chromatogram-class.html b/reference/Chromatogram-class.html index 947b5786..de19a829 100644 --- a/reference/Chromatogram-class.html +++ b/reference/Chromatogram-class.html @@ -9,8 +9,6 @@ - -
    - - -
    @@ -75,7 +67,6 @@

    Representation of chromatographic MS data

    Source: R/functions-Chromatogram.R, R/methods-Chromatogram.R
    -

    The Chromatogram class is designed to store chromatographic MS data, i.e. pairs of retention time and intensity @@ -85,7 +76,6 @@

    Representation of chromatographic MS data

    MSnExp objects extracting chromatograms should be used instead (i.e. the chromatogram() method).

    - 
    Chromatogram(
   rtime = numeric(),
@@ -183,173 +173,111 @@ 
    Representation of chromatographic MS data
    
 # S4 method for class 'Chromatogram'
 transformIntensity(object, FUN = identity)
    -

    Arguments

    rtime

    for Chromatogram: numeric with the retention times (length has to be equal to the length of intensity).

    - -
    intensity

    for Chromatogram: numeric with the intensity values (length has to be equal to the length of rtime). For filterIntensity: numeric(1) or function to use to filter intensities. See description for details.

    - -
    mz

    for Chromatogram: numeric(2) representing the mz value range (min, max) on which the chromatogram was created. This is supposed to contain the real range of mz values in contrast to filterMz. If not applicable use mzrange = c(0, 0).

    - -
    filterMz

    for Chromatogram: numeric(2) representing the mz value range (min, max) that was used to filter the original object on m/z dimension. If not applicable use filterMz = c(0, 0).

    - -
    precursorMz

    for Chromatogram: numeric(2) for SRM/MRM transitions. Represents the mz of the precursor ion. See details for more information.

    - -
    productMz

    for Chromatogram: numeric(2) for SRM/MRM transitions. Represents the mz of the product. See details for more information.

    - -
    fromFile

    for Chromatogram: integer(1) the index of the file within the OnDiskMSnExp or MSnExp from which the chromatogram was extracted.

    - -
    aggregationFun

    for Chromatogram: character string specifying the function that was used to aggregate intensity values for the same retention time across the mz range. Supported are "sum" (total ion chromatogram), "max" (base peak chromatogram), "min" and "mean".

    - -
    msLevel

    for Chromatogram: integer(1) with the MS level from which the chromatogram was extracted.

    - -
    object

    Chromatogram object.

    - -
    filter

    for mz: logical(1) defining whether the m/z range to filter the originating object (e.g. MSnExp object) should be returned or the m/z range of the actual data. Defaults to filter = FALSE.

    - -
    x

    Chromatogram object.

    - -
    rt

    for filterRt: numeric(2) defining the lower and upper retention time to which the Chromatogram should be subsetted.

    - -
    all

    for clean: logical(1) whether all 0 intensities should be removed. Defaults to all = FALSE. See clean() for details.

    - -
    na.rm

    for clean: if all NA intensities should be removed before cleaning the Chromatogram. Defaults to clean = FALSE.

    - -
    col

    for plot: the color to be used for plotting.

    - -
    lty

    for plot: the line type. See help page of plot in the graphics package for details.

    - -
    type

    for plot: the type of plot. See help page of plot in the graphics package for details.

    - -
    xlab

    for plot: the x-axis label.

    - -
    ylab

    for plot: the y-axis label.

    - -
    main

    for plot: the plot title. If not provided the mz range will be used as plot title.

    - -
    ...

    for plot: additional arguments to be passed to the base plot function. For filterIntensity: additional parameters passed along to the function provided with intensity. For compareChromatograms: ignored

    - -
    binSize

    for bin: numeric(1) with the size of the bins (in seconds). Defaults to binSize = 0.5.

    - -
    breaks

    for bin: numeric defining the bins. Usually not required as the function calculates the bins automatically based on binSize.

    - -
    fun

    for bin: function to be used to aggregate the intensity values falling within each bin. Defaults to fun = max.

    - -
    method

    character(1). For normalise: defining whether each chromatogram should be normalized to its maximum signal (method = "max") or total signal (method = "sum"). For alignRt: aligning approach that should be used (see description). Defaults to method = "closest".

    - -
    y

    for alignRt: Chromatogram against which x should be aligned against.

    - -
    ALIGNFUN

    for compareChromatograms: function to align chromatogram x against chromatogram y. Defaults to alignRt.

    - -
    ALIGNFUNARGS

    list of parameters to be passed to ALIGNFUN.

    - -
    FUN

    for compareChromatograms: function to calculate a similarity score on the intensity values of the compared and aligned chromatograms. Defaults to FUN = cor. For transformIntensity: function to transform chromatograms' intensity values. Defaults to FUN = identity.

    - -
    FUNARGS

    for compareChromatograms: list with additional parameters for FUN. Defaults to FUNARGS = list(use = "pairwise.complete.obs").

    -

    Details

    @@ -366,9 +294,6 @@

    Details

    Object creation

    - - -

    Chromatogram objects can be extracted from an MSnExp or OnDiskMSnExp object with the chromatogram() function.

    Alternatively, the constructor function Chromatogram can be used, which @@ -377,8 +302,6 @@

    Object creation

    Data access and coercion

    - -

    • aggregationFun: gets the aggregation function used to create the Chromatogram.

    • as.data.frame: returns a data.frame with columns "rtime" and @@ -402,8 +325,6 @@

      Data access and coercion

    Data subsetting and filtering

    - -

    • filterRt: filter/subset the Chromatogram to the specified retention time range (defined with parameter rt).

    • filterIntensity: filter a Chromatogram() object removing data @@ -418,8 +339,6 @@

      Data subsetting and filtering

    Data processing and manipulation

    - -

    • alignRt: Aligns chromatogram x against chromatogram y. The resulting chromatogram has the same length (number of data points) than y and the same retention times thus allowing to perform any pair-wise comparisons @@ -468,8 +387,6 @@

      Data processing and manipulation

    Data visualization

    - -

    • plot: plots a Chromatogram object.

    @@ -482,7 +399,6 @@

    See also

    Author

    Johannes Rainer

    -

    Examples

    
@@ -642,22 +558,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/FeatComp-class.html b/reference/FeatComp-class.html index 37269870..81e682c9 100644 --- a/reference/FeatComp-class.html +++ b/reference/FeatComp-class.html @@ -3,8 +3,6 @@ - -
    - - -

    Class "FeatComp"

    -
    -

    Comparing feature names of two comparable MSnSet instances.

    - -

    Objects from the Class

    - -

    Objects can be created with compfnames. The method compares the feature names of two objects of class "MSnSet". It prints a summary matrix of common and unique feature names and invisibly @@ -95,37 +81,24 @@

    Slots

    name of the compared features. By convention, "all" is used when all feature names are used; otherwise, the respective levels of the feature variables fcol1 and fcol2.

    - -
    common:

    Object of class "character" with the common feature names.

    - -
    unique1:

    Object of class "character" with the features unique to the first MSnSet (x in compfname).

    - -
    unique2:

    Object of class "character" with the features unique to the seconn MSnSet (y in compfname).

    - -
    all:

    Object of class "logical" defining if all features of only a subset were compared. One expects that name == "all" when all is TRUE.

    - - -

    Methods

    - -

    Accessors names, common, unique1 and unique2 can be used to access the respective FeatComp slots.

    @@ -142,8 +115,6 @@

    Methods

    FeatComp object is returned instead of a list of length 1. The verbose logical controls if a summary table needs to be printed (default is TRUE).

    - -
    compfnames

    signature(x = "list", y = "missing", ...): when x is a list of MSnSet instances, @@ -151,14 +122,9 @@

    Methods

    x. Additional parameters fcol1, fcol2, simplify and verbose are passed to the pairwise comparison method.

    - -
    show

    signature(object = "FeatComp"): prints a summary of the object.

    - - -

    Author

    @@ -168,12 +134,11 @@

    Author

    See also

    averageMSnSet to compuate an average MSnSet.

    -

    Examples

    library("pRolocdata")
 #> 
-#> This is pRolocdata version 1.41.0.
+#> This is pRolocdata version 1.42.0.
 #> Use 'pRolocdata()' to list available data sets.
 data(tan2009r1)
 data(tan2009r2)
@@ -269,22 +234,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/FeaturesOfInterest-class.html b/reference/FeaturesOfInterest-class.html index 6fd852a1..3459bd4b 100644 --- a/reference/FeaturesOfInterest-class.html +++ b/reference/FeaturesOfInterest-class.html @@ -1,6 +1,5 @@ Features of Interest — FeaturesOfInterest-class • MSnbaseContainer for multiple Chromatogram objects main = NULL, ... ) - # S4 method for class 'MChromatograms' phenoData(object) - # S4 method for class 'MChromatograms' pData(object) - # S4 method for class 'MChromatograms,data.frame' pData(object) <- value - # S4 method for class 'MChromatograms' $(x, name) - # S4 method for class 'MChromatograms' $(x, name) <- value - # S4 method for class 'MChromatograms' colnames(x) <- value - # S4 method for class 'MChromatograms' sampleNames(object) - # S4 method for class 'MChromatograms,ANY' sampleNames(object) <- value - # S4 method for class 'MChromatograms' isEmpty(x) - # S4 method for class 'MChromatograms' featureNames(object) - # S4 method for class 'MChromatograms' featureNames(object) <- value - # S4 method for class 'MChromatograms' featureData(object) - # S4 method for class 'MChromatograms,ANY' featureData(object) <- value - # S4 method for class 'MChromatograms' fData(object) - # S4 method for class 'MChromatograms,ANY' fData(object) <- value - # S4 method for class 'MChromatograms' fvarLabels(object) - # S4 method for class 'MChromatograms' rownames(x) <- value - # S4 method for class 'MChromatograms' precursorMz(object) - # S4 method for class 'MChromatograms' productMz(object) - # S4 method for class 'MChromatograms' mz(object) - # S4 method for class 'MChromatograms' polarity(object) - # S4 method for class 'MChromatograms' bin(x, binSize = 0.5, breaks = numeric(), fun = max) - # S4 method for class 'MChromatograms' clean(object, all = FALSE, na.rm = FALSE) - # S4 method for class 'MChromatograms' normalize(object, method = c("max", "sum")) - # S4 method for class 'MChromatograms' filterIntensity(object, intensity = 0, ...) - # S4 method for class 'MChromatograms,Chromatogram' alignRt(x, y, method = c("closest", "approx"), ...) - # S4 method for class 'MChromatograms' c(x, ...) - # S4 method for class 'MChromatograms,missing' compareChromatograms( x, @@ -193,7 +151,6 @@

    Container for multiple Chromatogram objects

    FUNARGS = list(use = "pairwise.complete.obs"), ... ) - # S4 method for class 'MChromatograms,MChromatograms' compareChromatograms( x, @@ -204,194 +161,123 @@

    Container for multiple Chromatogram objects

    FUNARGS = list(use = "pairwise.complete.obs"), ... ) - # S4 method for class 'MChromatograms' transformIntensity(object, FUN = identity)
    -

    Arguments

    data

    for MChromatograms: a list of Chromatogram() objects.

    - -
    phenoData

    for MChromatograms: either a data.frame, AnnotatedDataFrame describing the phenotypical information of the samples.

    - -
    featureData

    for MChromatograms: either a data.frame or AnnotatedDataFrame with additional information for each row of chromatograms.

    - -
    ...

    for MChromatograms: additional parameters to be passed to the matrix constructor, such as nrow, ncol and byrow. For compareChromatograms: ignored.

    - -
    object

    a MChromatograms object.

    - -
    x

    for all methods: a MChromatograms object.

    - -
    i

    for [: numeric, logical or character defining which row(s) to extract.

    - -
    j

    for [: numeric, logical or character defining which columns(s) to extract.

    - -
    drop

    for [: logical(1) whether to drop the dimensionality of the returned object (if possible). The default is drop = FALSE, i.e. each subsetting returns a MChromatograms object (or a Chromatogram object if a single element is extracted).

    - -
    value

    for [<-: the replacement object(s). Can be a list of [Chromatogram()objects or, if length ofiandjare 1, a singleChromatogram` object.

    For `pData<-`: a `data.frame` with the number of rows matching
 the number of columns of `object`.
-
-For `colnames`: a `character` with the new column names.

    - - +For `colnames`: a `character` with the new column names.

    col

    for plot: the color to be used for plotting. Either a vector of length 1 or equal to ncol(x).

    - -
    lty

    for plot: the line type (see plot in the graphics package for more details). Can be either a vector of length 1 or of length equal to ncol(x).

    - -
    type

    for plot: the type of plot (see plot from the graphics package for more details). Can be either a vector of length 1 or of length equal to ncol(x).

    - -
    xlab

    for plot: the x-axis label.

    - -
    ylab

    for plot: the y-axis label.

    - -
    main

    for plot: the plot title. If not provided the mz range will be used as plot title.

    - -
    name

    for $, the name of the pheno data column.

    - -
    binSize

    for bin: numeric(1) with the size of the bins (in seconds).

    - -
    breaks

    For bin: numeric defining the bins. Usually not required as the function calculates the bins automatically based on binSize and the retention time range of chromatograms in the same row.

    - -
    fun

    for bin: function to be used to aggregate the intensity values falling within each bin.

    - -
    all

    for clean: logical(1) whether all 0-intensities should be removed (all = TRUE), or whether 0-intensities adjacent to peaks should be kept (all = FALSE; default).

    - -
    na.rm

    for clean: logical(1) whether all NA intensities should be removed prior to clean 0-intensity data points.

    - -
    method

    character(1). For normalise: defining whether each chromatogram should be normalized to its maximum signal (method = "max") or total signal (method = "sum"). For alignRt: alignment methods (see documentation for alignRt in the Chromatogram() help page. Defaults to method = "closest".

    - -
    intensity

    for filterIntensity: numeric(1) or function to use to filter intensities. See description for details.

    - -
    y

    for alignRt: a Chromatogram() object against which x should be aligned against.

    - -
    ALIGNFUN

    for compareChromatograms: function to align chromatogram x against chromatogram y. Defaults to alignRt.

    - -
    ALIGNFUNARGS

    list of parameters to be passed to ALIGNFUN.

    - -
    FUN

    for transformIntensity: function to transform chromatograms' intensity values. Defaults to FUN = identity.

    - -
    FUNARGS

    for compareChromatograms: list with additional parameters for FUN. Defaults to FUNARGS = list(use = "pairwise.complete.obs").

    -

    Value

    - -

    For [: the subset of the MChromatograms object. If a single element is extracted (e.g. if i and j are of length 1) a Chromatogram() object is returned. Otherwise (if drop = FALSE, the default, is specified) a MChromatograms

    - -

    object is returned. If drop = TRUE is specified, the method returns a list of Chromatogram objects.

    - - 

    For `phenoData`: an `AnnotatedDataFrame` representing the
 pheno data of the object.
-
-For `pData`: a `data.frame` representing the pheno data of
-the object.
-
-For `$`: the value of the corresponding column in the pheno data
-table of the object.
-
-For all other methods see function description.

    - - +For `pData`: a `data.frame` representing the pheno data of +the object. +For `$`: the value of the corresponding column in the pheno data +table of the object. +For all other methods see function description.

    Details

    @@ -404,17 +290,12 @@

    Details

    Object creation

    - - -

    MChromatograms are returned by a chromatogram() function from an MSnExp or OnDiskMSnExp. Alternatively, the MChromatograms constructor function can be used.

    Data access

    - -

    Data subsetting, combining and filtering

    - -

    Data processing and manipulation

    - -

    Data visualization

    - -
    -

    Examples

    ## Creating some chromatogram objects to put them into a MChromatograms object
@@ -643,22 +517,12 @@ 
    Examples
    - - - - - - - - diff --git a/reference/MIAPE-class.html b/reference/MIAPE-class.html index 1f9921d5..9de61ba1 100644 --- a/reference/MIAPE-class.html +++ b/reference/MIAPE-class.html @@ -4,8 +4,6 @@ - -
    - - -

    The "MIAPE" Class for Storing Proteomics Experiment Information

    -
    -

    The Minimum Information About a Proteomics Experiment. The current implementation is based on the MIAPE-MS 2.4 document.

    - -

    Slots

    title:

    Object of class character containing a single-sentence experiment title.

    -
    abstract:

    Object of class character containing an abstract describing the experiment.

    -
    url:

    Object of class character containing a URL for the experiment.

    -
    pubMedIds:

    Object of class character listing strings of PubMed identifiers of papers relevant to the dataset.

    -
    samples:

    Object of class list containing information about the samples.

    -
    preprocessing:

    Object of class list containing information about the pre-processing steps used on the raw data from this experiment.

    -
    other:

    Object of class list containing other information for which none of the above slots applies.

    -
    dateStamp:

    Object of class character, giving the date on which the work described was initiated; given in the standard 'YYYY-MM-DD' format (with hyphens).

    -
    name:

    Object of class character containing the name of the (stable) primary contact person for this data set; this could be the experimenter, lab head, line manager, ...

    -
    lab:

    Object of class character containing the laboratory where the experiment was conducted.

    -
    contact:

    Object of class character containing contact information for lab and/or experimenter.

    -
    email:

    Object of class character containing tmail contact information for the primary contact person (see name above).

    -
    instrumentModel:

    Object of class character indicating the model of the mass spectrometer used to generate the data.

    -
    instrumentManufacturer:

    Object of class character indicating the manufacturing company of the mass spectrometer.

    -
    instrumentCustomisations:

    Object of class character describing any significant (i.e. affecting behaviour) deviations from the manufacturer's specification for the mass spectrometer.

    -
    softwareName:

    Object of class character with the instrument management and data analysis package(s) name(s).

    -
    softwareVersion:

    Object of class character with the instrument management and data analysis package(s) version(s).

    -
    switchingCriteria:

    Object of class character describing the list of conditions that cause the switch from survey or zoom mode (MS1) to or tandem mode (MSn where n > 1); e.g. 'parent - ion'' mass lists, neutral loss criteria and so on [applied for + ion” mass lists, neutral loss criteria and so on [applied for tandem MS only].

    -
    isolationWidth:

    Object of class numeric describing, for tandem instruments, the total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion m/z, provided for all levels or by MS level.

    -
    parameterFile:

    Object of class character giving the location and name under which the mass spectrometer's parameter settings file for the run is stored, if available. Ideally this should be a URI+filename, or most preferably an LSID, where feasible.

    -
    ionSource:

    Object of class character describing the ion source (ESI, MALDI, ...).

    -
    ionSourceDetails:

    Object of class character describing the relevant details about the ion source. See MIAPE-MI docuement for more details.

    -
    analyser:

    Object of class character describing the analyzer type (Quadrupole, time-of-flight, ion trap, ...).

    -
    analyserDetails:

    Object of class character describing the relevant details about the analyzer. See MIAPE-MI document for more details.

    -
    collisionGas:

    Object of class character describing the composition of the gas used to fragment ions in the collision cell.

    -
    collisionPressure:

    Object of class numeric providing the pressure (in bars) of the collision gas.

    -
    collisionEnergy:

    Object of class character specifying for the process of imparting a particular impetus to @@ -212,101 +174,76 @@

    Slots

    collision energies are also provided for individual "Spectrum2" instances, and is the preferred way of accessing this data.

    -
    detectorType:

    Object of class character describing the type of detector used in the machine (microchannel plate, channeltron, ...).

    -
    detectorSensitivity:

    Object of class character giving and appropriate measure of the sensitivity of the described detector (e.g. applied voltage).

    - -

    Methods

    The following methods as in "MIAME":

    abstract(MIAPE):

    An accessor function for abstract.

    -
    expinfo(MIAPE):

    An accessor function for name, lab, contact, title, and url.

    -
    notes(MIAPE), notes(MIAPE) <- value:

    Accessor - functions for other. notes(MIAME) <- character + functions for other. notes(MIAME) <- character appends character to notes; use notes(MIAPE) <- list to replace the notes entirely.

    -
    otherInfo(MIAPE):

    An accessor function for other.

    -
    preproc(MIAPE):

    An accessor function for preprocessing.

    -
    pubMedIds(MIAPE), pubMedIds(MIAME) <- value:

    Accessor function for pubMedIds.

    -
    expemail(MIAPE):
    -

    An accessor function for +

    An accessor function for email slot.

    -
    exptitle(MIAPE):

    An accessor function for title slot.

    -
    analyzer(MIAPE):

    An accessor function for analyser slot. analyser(MIAPE) is also available.

    -
    analyzerDetails(MIAPE):

    An accessor function for analyserDetails slot. analyserDetails is also available.

    -
    detectorType(MIAPE):

    An accessor function for detectorType slot.

    -
    ionSource(MIAPE):

    An accessor function for ionSource slot.

    -
    ionSourceDetails(MIAPE):

    An accessor function for ionSourceDetails slot.

    -
    instrumentModel(MIAPE):

    An accessor function for instrumentModel slot.

    -
    instrumentManufacturer(MIAPE):

    An accessor function for instrumentManufacturer slot.

    -
    instrumentCustomisations(MIAPE):

    An accessor function for instrumentCustomisations slot.

    -
    as(,"MIAME"):

    Coerce the object from MIAPE to MIAME class. Used when converting an MSnSet into an ExpressionSet.

    - -

    MIAPE-specific methods, including MIAPE-MS meta-data:

    show(MIAPE):

    Displays the experiment data.

    -
    msInfo(MIAPE):

    Displays 'MIAPE-MS' information.

    - -

    Extends

    @@ -323,28 +260,17 @@

    References

    Author

    Laurent Gatto <lg390@cam.ac.uk>

    -
    - - - - - - - - diff --git a/reference/MSmap-class.html b/reference/MSmap-class.html index 897e10dc..457d4e54 100644 --- a/reference/MSmap-class.html +++ b/reference/MSmap-class.html @@ -5,8 +5,6 @@ - -
    - - -

    Class MSmap

    -
    -

    A class to store mass spectrometry data maps, i.e intensities collected along the M/Z and retention time space during a mass spectrometry acquisition.

    - -

    Objects from the Class

    Objects can be created with the MSmap constructor. The - constructor has the following arguments:

    + constructor has the following arguments:

    object

    An object created by mzR::openMSfile or an instance of class OnDiskMSnExp. If the latter contains data from multiple files, a warning will be issued and the first one will be used.

    - -
    lowMz

    A numeric of length 1 defining the lower bound of the M/Z range of the MS map.

    - -
    highMz

    A numeric of length 1 defining the upper bound of the M/Z range of the MS map.

    - -
    resMz

    The resolution along the M/Z range.

    - -
    hd

    An optional data.frame as produced by mzR::header(object). If missing, will be computer within the function. Ignored when object is an OnDiskMSnExp.

    - -
    zeroIsNA

    Set 0 intensities to NA. This can be used to clarify the 3 dimensional plot produce by plot3D.

    - -

    Slots

    call:

    Object of class "call" - the call used to generate the instance.

    -
    map:

    Object of class "matrix" containing the actual MS map.

    -
    mz:

    Object of class "numeric" with the M/Z sampling bins.

    -
    res:

    Object of class "numeric" storing the the M/Z resolution used to create the map.

    -
    rt:

    Object of class "numeric" with the retention times of the map spectra.

    -
    ms:

    Object of class "numeric" with the MS levels of the spectra.

    -
    t:

    Object of class "logical" indicating if the instance has been transposed.

    -
    filename:

    Object of class "character" specifying the filename of the original raw MS data.

    - -

    Methods

    @@ -159,64 +126,50 @@

    Methods

    signature(from = "MSmap", to = "data.frame"): convert the MSmap instance in a data.frame. Useful for plotting with lattice or ggplot2.

    -
    fileName

    signature(object = "MSmap"): returns the raw data filename.

    -
    msLevel

    signature(object = "MSmap"): returns the MS level of the map spectra.

    -
    msMap

    signature(object = "MSmap"): returns the actual map matrix.

    -
    mz

    signature(object = "MSmap", ...): returns the M/Z values of the map. Additional arguments are currently ignored.

    -
    rtime

    signature(object = "MSmap", ...): returns retention time values of the map. Additional arguments are currently ignored.

    -
    mzRes

    signature(object = "MSmap"): returns the resolution with which the sample along the M/Z range was done.

    -
    dim

    signature(x = "MSmap"): returns the dimensions of the map. ncol and nrow return the number of columns and rows respectively.

    -
    t

    signature(x = "MSmap"): transposes the map.

    -
    show

    signature(object = "MSmap"): prints a summary of the map.

    -
    plot

    signature(x = "MSmap", allTicks = "logical"): produces an image of the map using lattice::levelplot. By default, allTicks is TRUE and all M/Z and retention times ticks of drawn. If set to FALSE, only 10 ticks in each dimension are plotted.

    -
    plot3D

    signature(object = "MSmap", rgl = "logical"): produces an three dimensional view of the map using lattice::cloude(..., type = "h"). If rgl is TRUE, the map is visualised on a rgl device and can be rotated with the mouse.

    - -

    Author

    Laurent Gatto <lg390@cam.ac.uk>

    -

    Examples

    
@@ -278,22 +231,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/MSnExp-class.html b/reference/MSnExp-class.html index c1ee9579..159d7dfb 100644 --- a/reference/MSnExp-class.html +++ b/reference/MSnExp-class.html @@ -16,8 +16,6 @@ - -
    - - -

    The 'MSnExp' Class for MS Data And Meta-Data

    -
    -

    The MSnExp class encapsulates data and meta-data for mass spectrometry experiments, as described in the slots @@ -99,8 +89,6 @@

    The 'MSnExp' Class for MS Data And Meta-Data

    file. See also the documentation in the mzR package that parses the raw data files and produces these data.

    - -

    Objects from the Class

    Objects can be created by calls of the form @@ -115,7 +103,6 @@

    Slots

    containing the MS spectra (see "Spectrum1" and "Spectrum2"). Slot is inherited from "pSet".

    -
    phenoData:

    Object of class "AnnotatedDataFrame" containing @@ -123,7 +110,6 @@

    Slots

    individual tags for an labelled MS experiment) See phenoData for more details. Slot is inherited from "pSet".

    -
    featureData:

    Object of class "AnnotatedDataFrame" containing variables @@ -132,13 +118,11 @@

    Slots

    "eSet"). See featureData for more details. Slot is inherited from "pSet".

    -
    experimentData:

    Object of class "MIAPE", containing details of experimental methods. See experimentData for more details. Slot is inherited from "pSet".

    -
    protocolData:

    Object of class "AnnotatedDataFrame" containing @@ -146,12 +130,10 @@

    Slots

    "eSet"). See protocolData for more details. Slot is inherited from "pSet".

    -
    processingData:

    Object of class "MSnProcess" that records all processing. Slot is inherited from "pSet".

    -
    .__classVersion__:

    Object of class "Versions" describing the versions of R, @@ -160,8 +142,6 @@

    Slots

    Slot is inherited from "pSet". Intended for developer use and debugging (inherited from "eSet").

    - -

    Extends

    @@ -177,25 +157,21 @@

    Methods

    bin

    signature(object = "MSnExp"): Bins spectra. See bin documentation for more details and examples.

    -
    clean

    signature(object = "MSnExp"): Removes unused 0 intensity data points. See clean documentation for more details and examples.

    -
    compareSpectra

    signature(x = "Spectrum", y = "missing"): Compares spectra. See compareSpectra documentation for more details and examples.

    -
    extractPrecSpectra

    signature(object = "MSnExp", prec = "numeric"): extracts spectra with precursor MZ value equal to prec and returns an object of class 'MSnExp'. See extractPrecSpectra documentation for more details and examples.

    - % \item{extractSpectra}{\code{signature(object = "MSnExp", selected = % "logical")}: extracts spectra corresponding to 'TRUE' in % \code{selected}. @@ -207,104 +183,80 @@

    Methods

    allows to restrict peak picking to spectra of certain MS level(s). See pickPeaks documentation for more details and examples.

    -
    estimateNoise

    signature(object = "MSnExp"): Estimates the noise in all profile spectra of object. See estimateNoise documentation for more details and examples.

    -
    plot

    signature(x = "MSnExp", y = "missing"): Plots the MSnExp instance. See plot.MSnExp documentation for more details.

    -
    plot2d

    signature(object = "MSnExp", ...): Plots retention time against precursor MZ for MSnExp instances. See plot2d documentation for more details.

    -
    plotDensity

    signature(object = "MSnExp", ...): Plots the density of parameters of interest. instances. See plotDensity documentation for more details.

    -
    plotMzDelta

    signature(object = "MSnExp", ...): Plots a histogram of the m/z difference betwee all of the highest peaks of all MS2 spectra of an experiment. See plotMzDelta documentation for more details.

    -
    quantify

    signature(object = "MSnExp"): Performs quantification for all the MS2 spectra of the MSnExp instance. See quantify documentation for more details. Also for OnDiskMSnExp objects.

    -
    removePeaks

    signature(object = "MSnExp"): Removes peaks lower that a threshold t. See removePeaks documentation for more details and examples.

    -
    removeReporters

    signature(object = "MSnExp", ...): Removes reporter ion peaks from all MS2 spectra of an experiment. See removeReporters documentation for more details and examples.

    -
    smooth

    signature(x = "MSnExp"): Smooths spectra. See smooth documentation for more details and examples.

    -
    addIdentificationData

    signature(object = "MSnExp", ...): Adds identification data to an experiment. See addIdentificationData documentation for more details and examples.

    - -
    removeNoId

    signature(object = "MSnExp", fcol = "pepseq", keep = NULL): Removes non-identified features. See removeNoId documentation for more details and examples.

    - -
    removeMultipleAssignment

    signature(object = "MSnExp", fcol = "nprot"): Removes protein groups (or feature belong to protein groups) with more than one member. The latter is defined by extracting a feature variable (default is "nprot"). Also removes non-identified features.

    - -
    idSummary

    signature(object = "MSnExp", ...): Prints a summary that lists the percentage of identified features per file (called coverage).

    - -
    show

    signature(object = "MSnExp"): Displays object content as text.

    - -
    isolationWindow

    signature(object = "MSnExp", ...): Returns the isolation window offsets for the MS2 spectra. See isolationWindow in the mzR package for details.

    - -
    trimMz

    signature(object = "MSnExp"): Trims the MZ range of all the spectra of the MSnExp instance. See trimMz documentation for more details and examples.

    - -
    isCentroided(object, k = 0.025, qtl = 0.9, verbose = TRUE)

    A heuristic assessing if the spectra in the @@ -323,108 +275,74 @@

    Methods

    advised to assign the majority result for MS1 and MS2 spectra, rather than results for individual spectra. See an example below.

    - -
    as

    signature(object = "MSnExp", "data.frame"): Coerces the MSnExp object to a four-column data.frame with columns "file" (file index in object), "rt" (retention time), "mz" (m/z values) and "i" (intensity values).

    - -
    as

    signature(object = "MSnExp", "MSpectra"): Coerces the MSnExp object to a MSpectra object with all feature annotations added as metadata columns (mcols).

    - - Clarifications regarding scan/acquisition numbers and indices: - A spectrumId (or spectrumID) is a vendor specific field in the mzML file that contains some information about the run/spectrum, e.g.: controllerType=0 controllerNumber=1 scan=5281 file=2. - acquisitionNum is a more a less sanitize spectrum id generated from the spectrumId field by mzR (see https://github.com/sneumann/mzR/blob/master/src/pwiz/data/msdata/MSData.cpp#L552-L580). - scanIndex is the mzR generated sequence number of the spectrum in the raw file (which doesn't have to be the same as the acquisitionNum). - See also this issue: https://github.com/lgatto/MSnbase/issues/525. - -

    Filtering and subsetting functions:

    filterRt

    signature(object = "MSnExp", rt = "numeric", msLevel. = "numeric"): Retains MS spectra of level msLevel. with a retention times within rt[1] and rt[2].

    - -
    filterMsLevel

    signature(object = "MSnExp", msLevel. = "numeric"): Retains MS spectra of level msLevel..

    - -
    filterPolarity

    signature(object = "MSnExp", polarity. = "numeric"): Retains MS spectra of polarity polarity..

    - -
    filterMz

    signature(object = "MSnExp", mz = "numeric", msLevel. = "numeric"). See filterMz for details.

    - -
    filterFile

    signature(object = "MSnExp", file): Retains MS data of files matching the file index or file name provided with parameter file.

    - -
    filterAcquisitionNum
    - -
    filterEmptySpectra

    signature(object = "MSnExp"): Remove empty spectra from object (see isEmpty).

    - -
    filterPrecursorScan

    signature(object = "MSnExp", acquisitionNum = "numeric"): Retain parent (e.g. MS1) and children scans (e.g. MS2) of acquisitionNum. See OnDiskMSnExp for an example.

    - -
    splitByFile

    signature(object = "MSnExp", f = "factor"): split a MSnExp object by file into a list of MSnExp objects given the grouping in factor f.

    - -
    filterPrecursorMz

    signature(object = "MSnExp", mz, ppm = 10): retain spectra with a precursor m/z equal or similar to the one defined with parameter mz. Parameter ppm allows to define an accepted difference between the provided m/z and the spectrum's m/z.

    - -
    filterIsolationWindow

    signature(object = "MSnExp", mz): retain spectra with isolation windows that contain (which m/z range contain) the specified m/z.

    - -

    References

    @@ -448,7 +366,6 @@

    See also

    write for the function to write the data to mzML or mzXML file(s).

    -

    Examples

    mzxmlfile <- dir(system.file("extdata",package="MSnbase"),
@@ -462,8 +379,8 @@ 
    Examples
    
 #>  Number of spectra: 5 
 #>  MSn retention times: 25:01 - 25:02 minutes
 #> - - - Processing information - - -
-#> Data loaded: Wed May  1 08:21:50 2024 
-#>  MSnbase version: 2.31.0 
+#> Data loaded: Wed May 15 16:29:12 2024 
+#>  MSnbase version: 2.31.1 
 #> - - - Meta data  - - -
 #> phenoData
 #>   rowNames: dummyiTRAQ.mzXML
@@ -484,22 +401,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/MSnProcess-class.html b/reference/MSnProcess-class.html index 78fe0e59..444e7bd7 100644 --- a/reference/MSnProcess-class.html +++ b/reference/MSnProcess-class.html @@ -6,8 +6,6 @@ - -
    - - -

    The "MSnProcess" Class

    -
    -

    MSnProcess is a container for MSnExp and MSnSet processing information. It records data files, processing steps, thresholds, analysis methods and times that have been applied to MSnExp or MSnSet instances.

    - -

    Slots

    files:

    Object of class "character" storing the raw data files used in experiment described by the "MSnProcess" instance.

    -
    processing:

    Object of class "character" storing all the processing steps and times.

    -
    merged:

    Object of class "logical" indicating whether spectra have been merged.

    -
    cleaned:

    Object of class "logical" indicating whether spectra have been cleaned. See clean for more details and examples.

    -
    removedPeaks:

    Object of class "character" describing whether peaks have been removed and which threshold was used. See removePeaks for more details and examples.

    -
    smoothed:

    Object of class "logical" indicating whether spectra have been smoothed.

    -
    trimmed:

    Object of class "numeric" documenting if/how the data has been trimmed.

    -
    normalised:

    Object of class "logical" describing whether and how data have been normalised.

    -
    MSnbaseVersion:

    Object of class "character" indicating the version of MSnbase.

    -
    .__classVersion__:

    Object of class "Versions" indicating the version of the MSnProcess instance. Intended for developer use and debugging.

    - - -

    Extends

    @@ -140,16 +116,12 @@

    Methods

    signature(object = "MSnProcess"): Returns the file names used in experiment described by the "MSnProcess" instance.

    -
    show

    signature(object = "MSnProcess"): Displays object content as text.

    -
    combine

    signature(x = "MSnProcess", y = "MSnProcess"): Combines multiple MSnProcess instances.

    - -

    Author

    @@ -164,7 +136,6 @@

    See also

    See the "MSnExp" and "MSnSet" classes that actually use MSnProcess as a slot.

    -

    Examples

    showClass("MSnProcess")
@@ -189,22 +160,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/MSnSet-class.html b/reference/MSnSet-class.html index 6a009ce1..129d816d 100644 --- a/reference/MSnSet-class.html +++ b/reference/MSnSet-class.html @@ -8,8 +8,6 @@ - -
    - - -

    The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

    -
    -

    The MSnSet holds quantified expression data for MS proteomics data and the experimental meta-data. @@ -83,12 +73,8 @@

    The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

    "ExpressionSet" class classically used for microarray data.

    - -

    Objects from the Class

    - -

    The constructor MSnSet(exprs, fData, pData) can be used to create MSnSet instances. Argument exprs is a matrix and fData and pData must be of class @@ -119,19 +105,13 @@

    Objects from the Class

    Slots

    - -

    qual:

    Object of class "data.frame" that records peaks data for each of the reporter ions to be used as quality metrics.

    - -
    processingData:

    Object of class "MSnProcess" that records all processing.

    - -
    assayData:

    Object of class "assayData" containing a matrix with equal with column number equal to @@ -141,8 +121,6 @@

    Slots

    class, exprs and assayData accessor for more details. This slot in indirectly inherited from "eSet".

    - -
    phenoData:

    Object of class "AnnotatedDataFrame" containing experimenter-supplied variables describing sample (i.e @@ -153,8 +131,6 @@

    Slots

    with pData and be replaced by a new valid (i.e. of compatible dimensions and row names) data.frame with pData()<-.

    - -
    featureData:

    Object of class "AnnotatedDataFrame" containing variables describing @@ -165,20 +141,14 @@

    Slots

    can be accessed as a data.frame with fData and be replaced by a new valid (i.e. of compatible dimensions and row names) data.frame with fData()<-.

    - -
    experimentData:

    Object of class "MIAPE", containing details of experimental methods (inherited from "eSet"). See experimentData and the "eSet" class for more details.

    - -
    annotation:

    not used here.

    - -
    protocolData:

    Object of class "AnnotatedDataFrame" containing @@ -186,8 +156,6 @@

    Slots

    "eSet"). See protocolData and the "eSet" class for more details.

    - -
    .__classVersion__:

    Object of class "Versions" describing the versions of R, @@ -195,8 +163,6 @@

    Slots

    "pSet" and MSnSet of the current instance. Intended for developer use and debugging (inherited indirectly from "eSet").

    - -

    Extends

    @@ -214,8 +180,6 @@

    Methods

    a numeric vector with acquisition number of each spectrum. The vector names are the corresponding spectrum names. The information is extracted from the object's featureData slot.

    - -
    fromFile

    fromFile(signature(object = "MSnSet")): get the index of the file (in fileNames(object)) from which the raw @@ -224,59 +188,39 @@

    Methods

    featureData slot.

    Returns a numeric vector with names corresponding to the spectrum names.

    - -
    dim

    signature(x = "MSnSet"): Returns the dimensions of object's assay data, i.e the number of samples and the number of features.

    - -
    fileNames

    signature(object = "MSnSet"): Access file names in the processingData slot.

    - -
    msInfo

    signature(object = "MSnSet"): Prints the MIAPE-MS meta-data stored in the experimentData slot.

    - -
    processingData

    signature(object = "MSnSet"): Access the processingData slot.

    - -
    show

    signature(object = "MSnSet"): Displays object content as text.

    - -
    qual

    signature(object = "MSnSet"): Access the reporter ion peaks description.

    - -
    purityCorrect

    signature(object = "MSnSet", impurities = "matrix"): performs reporter ions purity correction. See purityCorrect documentation for more details.

    - -
    normalise

    signature(object = "MSnSet"): Performs MSnSet normalisation. See normalise for more details.

    - -
    t

    signature(x = "MSnSet"): Returns a transposed MSnSet object where features are now aligned along columns and samples along rows and the phenoData and featureData slots have been swapped. The protocolData slot is always dropped.

    - -
    as(,"ExpressionSet")

    signature(x = "MSnSet"): Coerce object from MSnSet to @@ -284,28 +228,20 @@

    Methods

    is converted to a MIAME instance. It is also possible to coerce an ExpressionSet to and MSnSet, in which case the experimentData slot is newly initialised.

    - -
    as(,"IBSpectra")

    signature(x = "MSnSet"): Coerce object from MSnSet to IBSpectra from the isobar package.

    - -
    as(,"data.frame")

    signature(x = "MSnSet"): Coerce object from MSnSet to data.frame. The MSnSet is transposed and the PhenoData slot is appended.

    - -
    as(,"SummarizedExperiment")

    signature(x = "MSnSet"): Coerce object from MSnSet to SummarizedExperiment. Only part of the metadata is retained. See addMSnSetMetadata and the example below for details.

    - -
    write.exprs

    signature(x = "MSnSet"): Writes expression values to a tab-separated file (default is tmp.txt). The @@ -313,15 +249,11 @@

    Methods

    featureData columns (as column names, column number or logical) to append on the right of the expression matrix. The following arguments are the same as write.table.

    - -
    combine

    signature(x = "MSnSet", y = "MSnSet", ...): Combines 2 or more MSnSet instances according to their feature names. Note that the qual slot and the processing information are silently dropped.

    - -
    topN

    signature(object = "MSnSet", groupBy, n = 3, fun, ..., verbose = isMSnbaseVerbose()): @@ -339,8 +271,6 @@

    Methods

    actual number of retained peptides out of n.

    A complete use case using topN and nQuants is detailed in the synapter package vignette.

    - -
    filterNA

    signature(object = "MSnSet", pNA = "numeric", pattern = "character", droplevels = "logical"): This method @@ -357,49 +287,34 @@

    Methods

    See the droplevels method below.

    See also the is.na.MSnSet and plotNA methods for missing data exploration.

    - -
    filterZero

    signature(object = "MSnSet", pNA = "numeric", pattern = "character", droplevels = "logical"): As filterNA, but for zeros.

    - -
    filterMsLevel

    signature(object = "MSnSet", msLevel. = "numeric", fcol = "character") Keeps only spectra with level msLevel., as defined by the fcol feature variable (default is "msLevel").

    - -
    log

    signature(object = "MSnSet", base = "numeric") Log transforms exprs(object) using base::log. base (defaults is e='exp(1)') must be a positive or complex number, the base with respect to which logarithms are computed.

    - -
    droplevels

    signature(x = "MSnSet", ...)Drops the unused factor levels in the featureData slot. See droplevels for details.

    - -
    impute

    signature(object = "MSnSet", ...) Performs data imputation on the MSnSet object. See impute for more details.

    - -
    trimws

    signature(object = "MSnSet", ...)Trim leading and/or trailing white spaces in the feature data slot. Also available for data.frame objects. See ?base::trimws for details.

    - - -

    Additional accessors for the experimental metadata (experimentData slot) are defined. See "MIAPE" for details.

    @@ -410,8 +325,6 @@

    Plotting

    signature(object = "MSnSet") Plots row standard deviations versus row means. See meanSdPlot (vsn package) for more details.

    - -
    image

    signature(x = "MSnSet", facetBy = "character", sOrderBy = "character", legend = "character", low = "character", @@ -436,8 +349,6 @@

    Plotting

    The code is based on Vlad Petyuk's vp.misc::image_msnset. The previous version of this method is still available through the image2 function.

    - -
    plotNA

    signature(object = "MSnSet", pNA = "numeric") @@ -448,8 +359,6 @@

    Plotting

    percentage of NA values in the full data set and the number of proteins retained. Default is 1/2. See also plotNA.

    - -
    MAplot

    signature(object = "MSnSet", log.it = "logical", base = "numeric", ...) @@ -462,37 +371,26 @@

    Plotting

    should be log-transformed (default is TRUE) using base. Further ... arguments will be passed to the respective functions.

    - -
    addIdentificationData

    signature(object = "MSnSet", ...): Adds identification data to a MSnSet instance. See addIdentificationData documentation for more details and examples.

    - -
    removeNoId

    signature(object = "MSnSet", fcol = "pepseq", keep = NULL): Removes non-identified features. See removeNoId documentation for more details and examples.

    - -
    removeMultipleAssignment

    signature(object = "MSnSet", fcol = "nprot"): Removes protein groups (or feature belong to protein groups) with more than one member. The latter is defined by extracting a feature variable (default is "nprot"). Also removes non-identified features.

    - -
    idSummary

    signature(object = "MSnSet", ...): Prints a summary that lists the percentage of identified features per file (called coverage).

    - - -

    Functions

    @@ -501,29 +399,21 @@

    Functions

    function updates object's featureData variable labels by appending label. By default, label is the variable name and the separator sep is ..

    - -
    updateSampleNames

    signature(object, label, sep) This function updates object's sample names by appending label. By default, label is the variable name and the separator sep is ..

    - -
    updateFeatureNames

    signature(object, label, sep) This function updates object's feature names by appending label. By default, label is the variable name and the separator sep is ..

    - -
    ms2df

    signature(x, fcols) Coerces the MSnSet instance to a data.frame. The direction of the data is retained and the feature variable labels that match fcol are appended to the expression values. See also as(x, "data.frame") above.

    - -
    addMSnSetMetadata

    signature(x, y) When coercing an MSnSet y to a SummarizedExperiment x @@ -534,9 +424,6 @@

    Functions

    the complete processingData, experimentData and protocolData slots. The downside of this is that MSnbase is now required to use the SummarizedExperiment object.

    - - -

    Author

    @@ -545,7 +432,6 @@

    Author

    See also

    -

    "eSet", "ExpressionSet" and quantify. MSnSet quantitation values and annotation can be exported to a file with @@ -553,7 +439,6 @@

    See also

    create and MSnSet using data available in a spreadsheet or data.frame.

    -

    Examples

    data(msnset)
@@ -678,7 +563,7 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> iTRAQ4 quantification by trapezoidation: Wed Apr  1 21:41:53 2015 
-#> Subset [55,4][6,4] Wed May  1 08:21:50 2024 
+#> Subset [55,4][6,4] Wed May 15 16:29:13 2024 
 #>  MSnbase version: 1.1.22 
 
 as(msnset, "ExpressionSet")
@@ -704,22 +589,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/MSnSetList-class.html b/reference/MSnSetList-class.html index edaa2017..4b6409ab 100644 --- a/reference/MSnSetList-class.html +++ b/reference/MSnSetList-class.html @@ -4,8 +4,6 @@ - -
    - - -

    Storing multiple related MSnSets

    -
    -

    A class for storing lists of MSnSet instances.

    - -

    Details

    - -

    There are two ways to store different sets of measurements pertaining an experimental unit, such as replicated measures of different conditions that were recorded over more than one MS @@ -107,16 +93,12 @@

    Details

    Objects from the Class

    - -

    Objects can be created and manipluated with:

    MSnSetList(x, log, featureDAta)

    The class constructor that takes a list of valid MSnSet instances as input x, an optional logging list, and an optional feature metadata data.frame.

    - -
    split(x, f)

    An MSnSetList can be created from an MSnSet instance. x is a single @@ -132,21 +114,14 @@

    Objects from the Class

    determine if x will be split along the features (rows) or sample (columns). Hence, the length of f must match exactly to either dimension.

    - -
    unsplit(value, f)

    The unsplit method reverses the effect of splitting the value MSnSet along the groups f.

    - -
    as(x, "MSnSetList")

    Where x is an instance of class MzTab. See the class documentation for details.

    - - -

    Slots

    @@ -154,77 +129,53 @@

    Slots

    Object of class list containing valid MSnSet instances. Can be extracted with the msnsets() accessor.

    - -
    log:

    Object of class list containing an object creation log, containing among other elements the call that generated the object. Can be accessed with objlog().

    - -
    featureData:

    Object of class DataFrame that stores metadata for each object in the x slot. The number of rows of this data.frame must be equal to the number of items in the x slot and their respective (row)names must be identical.

    - -
    .__classVersion__:

    The version of the instance. For development purposes only.

    - -

    Methods

    "[["

    Extracts a single MSnSet at position.

    - -
    "["

    Extracts one of more MSnSets as MSnSetList.

    - -
    length

    Returns the number of MSnSets.

    - -
    names

    Returns the names of MSnSets, if available. The replacement method is also available.

    -
    show

    Display the object by printing a short summary.

    - -
    lapply(x, FUN, ...)

    Apply function FUN to each element of the input x. If the application of FUN returns and MSnSet, then the return value is an MSnSetList, otherwise a list

    . -
    sapply(x, FUN, ..., simplify = TRUE, USE.NAMES = TRUE)

    A lapply wrapper that simplifies the ouptut to a vector, matric or array is possible. See ?base::sapply for details.

    . -
    fData

    Returns the features metadata featureData slot.

    - -
    fData<-

    Features metadata featureData replacement method.

    - - -

    See also

    @@ -235,7 +186,6 @@

    See also

    Author

    Laurent Gatto <lg390@cam.ac.uk>

    -

    Examples

    library("pRolocdata")
@@ -399,22 +349,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/MSnbaseOptions.html b/reference/MSnbaseOptions.html index ae87f78a..4fa70115 100644 --- a/reference/MSnbaseOptions.html +++ b/reference/MSnbaseOptions.html @@ -11,13 +11,10 @@ methods of OnDiskMSnExp that load data from the original files (such as spectrapply()). Users experiencing data I/O errors (observed mostly on macOS systems) should set this option to FALSE. - "> - -
    - - -
    @@ -82,7 +73,6 @@

    MSnbase options

    Source: R/options.R
    -

    MSnbase defined a few options globally using the standard R options mechanism. The current values of these options can be @@ -96,7 +86,6 @@

    MSnbase options

    spectrapply()). Users experiencing data I/O errors (observed mostly on macOS systems) should set this option to FALSE.

    - 
    MSnbaseOptions()
 
@@ -110,17 +99,13 @@ 
    MSnbase options
    
 
 isMSnbaseFastLoad()
    -

    Arguments

    opt

    The value of the new option

    -

    Value

    - -

    A list of MSnbase options and the single option values for the individual accessors.

    @@ -132,28 +117,17 @@

    Details

    without argument, the verbosity setter inverts the current value of the option.

    -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/MSpectra.html b/reference/MSpectra.html index 9a5656a7..0c68d37e 100644 --- a/reference/MSpectra.html +++ b/reference/MSpectra.html @@ -13,8 +13,6 @@ - -
    - - -
    @@ -79,7 +71,6 @@

    List of Spectrum objects along with annotations

    Source: R/DataClasses.R, R/functions-MSpectra.R, R/methods-MSpectra.R
    -

    MSpectra (Mass Spectra) objects allow to collect one or more Spectrum object(s) (Spectrum1 or Spectrum2) in @@ -93,7 +84,6 @@

    List of Spectrum objects along with annotations

    metadata columns present in mcols are exported as additional fields with the capitalized column names used as field names (see examples below).

    - 
    MSpectra(..., elementMetadata = NULL)
 
@@ -191,85 +181,55 @@ 
    List of Spectrum objects along with annotations
    
 # S4 method for class 'MSpectra'
 filterMsLevel(object, msLevel.)
    -

    Arguments

    ...

    For MSpectra: Spectrum object(s) or a list of Spectrum objects. For all other methods optional arguments passed along.

    - -
    elementMetadata

    For MSpectra: DataFrame with optional information that should be added as metadata information (mcols) to the object. The number of rows has to match the number of Spectrum objects, each row is expected to represent additional metadata information for one spectrum.

    - -
    object

    For all functions: a MSpectra object.

    - -
    x

    For all functions: a MSpectra object.

    - -
    con

    For writeMgfData: character(1) defining the file name of the MGF file.

    - -
    COM

    For writeMgfData: optional character(1) providing a comment to be added to the file.

    - -
    TITLE

    For writeMgfData: optional character(1) defining the title for the MGF file.

    - -
    all

    For clean: if FALSE original 0-intensity values are retained around peaks.

    - -
    msLevel.

    For clean, removePeaks, filterMz, pickPeaks: optionally specify the MS level(s) of the spectra on which the operation should be performed. For filterMsLevels: MS level(s) to which the MSpectra should be reduced.

    - -
    t

    For removePeaks: numeric(1) specifying the threshold below which intensities are set to 0.

    - -
    mz

    For filterMz: numeric(2) defining the lower and upper m/z for the filter. See filterMz() for details.

    - -
    halfWindowSize

    For pickPeaks and smooth: see pickPeaks() and smooth() for details.

    - -
    method

    For pickPeaks and smooth: see pickPeaks() and smooth() for details.

    - -
    SNR

    For pickPeaks: see pickPeaks() for details.

    - -
    refineMz

    For pickPeaks: see pickPeaks() for details.

    -

    Details

    @@ -279,18 +239,12 @@

    Details

    Constructor

    - - -

    New MSpectra can be created with the MSpectra(...) function where ... can either be a single Spectrum object or a list of Spectrum objects (Spectrum1 and/or Spectrum2).

    Accessing spectrum attributes

    - - -

    These methods allow to access the attributes and values of the individual Spectrum (Spectrum1 or Spectrum2) objects within the list.

    • mz return the m/z values of each spectrum as a list of numeric vectors.

      • @@ -327,8 +281,6 @@

      Accessing spectrum attributes

    Data manipulation methods

    - -

    • clean cleans each spectrum. See clean() for more details.

    • pickPeaks performs peak picking to generate centroided spectra. See pickPeaks() for more details.

      • @@ -338,8 +290,6 @@

      Data manipulation methods

    Filtering and subsetting

    - -

    • [ can be used to subset the MSpectra object.

    • filterMsLevel filters MSpectra to retain only spectra from certain MS level(s).

      • @@ -350,7 +300,6 @@

      Filtering and subsetting

      Author

      Johannes Rainer

    -

    Examples

    
@@ -511,7 +460,7 @@ 
    Examples
    
 ## Evaluate the written output. The ID of each spectrum (defined in the
 ## "id" metadata column) is exported as field "ID".
 readLines(tmpf)
-#>  [1] "COM=Experimentexported by MSnbase on Wed May  1 08:21:58 2024"   
+#>  [1] "COM=Experimentexported by MSnbase on Wed May 15 16:29:21 2024"   
 #>  [2] "BEGIN IONS"                                                      
 #>  [3] "SCANS=NA"                                                        
 #>  [4] "TITLE=msLevel 1; retentionTime ; scanNum NA"                     
@@ -541,7 +490,7 @@ 
    Examples
    
 
 writeMgfData(spl, tmpf)
 readLines(tmpf)
-#>  [1] "COM=Experimentexported by MSnbase on Wed May  1 08:21:58 2024"   
+#>  [1] "COM=Experimentexported by MSnbase on Wed May 15 16:29:21 2024"   
 #>  [2] "BEGIN IONS"                                                      
 #>  [3] "SCANS=NA"                                                        
 #>  [4] "TITLE=msLevel 1; retentionTime ; scanNum NA"                     
@@ -575,22 +524,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/MzTab-class.html b/reference/MzTab-class.html index e5327bee..d5ab1fa6 100644 --- a/reference/MzTab-class.html +++ b/reference/MzTab-class.html @@ -1,6 +1,5 @@ Parse MzTab files — MzTab-class • MSnbasefeatureData slot.

    Returns a numeric vector with names corresponding to the spectrum names.

    - -
    intensity

    intensity(signature(object="OnDiskMSnExp")): return the intensities from each spectrum in the data @@ -279,8 +243,6 @@

    Getter/setter methods

    original file).

    The method returns a list of numeric intensity values. Each list element represents the intensities from one spectrum.

    - -
    ionCount

    ionCount(signature(object="OnDiskMSnExp", BPPARAM=bpparam())): @@ -293,37 +255,27 @@

    Getter/setter methods

    original file).

    Returns a numeric vector with names corresponding to the spectrum names.

    - -
    isolationWindowLowerMz

    isolationWindowLowerMz(object = "OnDiskMSnExp"): return the lower m/z boundary for the isolation window.

    Returns a numeric vector of length equal to the number of spectra with the lower m/z value of the isolation window or NA if not specified in the original file.

    - -
    isolationWindowUpperMz

    isolationWindowUpperMz(object = "OnDiskMSnExp"): return the upper m/z boundary for the isolation window.

    Returns a numeric vector of length equal to the number of spectra with the upper m/z value of the isolation window or NA if not specified in the original file.

    - -
    length

    length(signature(object="OnDiskMSnExp")): Returns the number of spectra of the current experiment.

    - -
    msLevel

    msLevel(signature(object = "OnDiskMSnExp")): extract the MS level from the spectra. The relevant information is extracted from the object's featureData slot.

    Returns a numeric vector with names corresponding to the spectrum names.

    - -
    mz

    mz(signature(object="OnDiskMSnExp")): return the M/Z values from each spectrum in the data @@ -337,8 +289,6 @@

    Getter/setter methods

    original file).

    The method returns a list of numeric M/Z values. Each list element represents the values from one spectrum.

    - -
    peaksCount

    peaksCount(signature(object="OnDiskMSnExp", scans="numeric"), BPPARAM=bpparam()): @@ -354,31 +304,23 @@

    Getter/setter methods

    original file).

    Returns a numeric vector with names corresponding to the spectrum names.

    - -
    polarity

    polarity(signature(object="OnDiskMSnExp")): returns a numeric vector with the polarity of the individual spectra in the data set. The relevant information is extracted from the featureData.

    - -
    rtime

    rtime(signature(object="OnDiskMSnExp")): extrac the retention time of the individual spectra in the data set (from the featureData).

    Returns a numeric vector with names corresponding to the spectrum names.

    - -
    scanIndex

    scanIndex(signature(object="OnDiskMSnExp")): get the spectra scan indices within the respective file. The relevant information is extracted from the object's featureData slot. Returns a numeric vector of indices with names corresponding to the spectrum names.

    - -
    smoothed,smoothed<-

    smoothed(signature(object="OnDiskMSnExp", msLevel. = "numeric")): whether individual spectra are smoothed or @@ -388,8 +330,6 @@

    Getter/setter methods

    smoothed(object) <- value to update the information, with value being a logical vector of length equal to the number of spectra in the experiment.

    - -
    spectra

    spectra(signature(object="OnDiskMSnExp"), BPPARAM=bpparam()): extract spectrum data from the individual files. This causes the @@ -405,8 +345,6 @@

    Getter/setter methods

    extraction.

    Returns a list of Spectrum1 objects with names corresponding to the spectrum names.

    - -
    tic

    tic(signature(object="OnDiskMSnExp"), initial = TRUE, BPPARAM = bpparam()): @@ -422,8 +360,6 @@

    Getter/setter methods

    BPPARAM parameter: see spectra method above.

    Returns a numeric vector with names corresponding to the spectrum names.

    - -
    bpi

    bpi(signature(object="OnDiskMSnExp"), initial = TRUE, BPPARAM = bpparam()): @@ -439,14 +375,10 @@

    Getter/setter methods

    BPPARAM parameter: see spectra method above.

    Returns a numeric vector with names corresponding to the spectrum names.

    - -
    featureNames

    tic(signature(object="OnDiskMSnExp")): return a character of length length(object) containing the feature names. A replacement method is also available.

    - -
    spectrapply

    spectrapply(signature(object = "OnDiskMSnExp"), FUN = NULL, BPPARAM = bpparam(), ...): applies the function FUN to each @@ -456,8 +388,6 @@

    Getter/setter methods

    BPPARAM allows to specify how and if parallel processing should be enabled.

    Returns a list with the result for each of spectrum.

    - -

    Data manipulation methods

    @@ -478,8 +408,6 @@

    Data manipulation methods

    The method returns an OnDiskMSnExp object.

    For more details see documentation of the clean method.

    - -
    normalize

    normalize(signature(object="OnDiskMSnExp"), method=c("max", "sum"), ...): @@ -488,8 +416,6 @@

    Data manipulation methods

    The method returns an OnDiskMSnExp object.

    For more details see documentation of the normalize method.

    - -
    removePeaks

    removePeaks(signature(object="OnDiskMSnExp"), t="min", verbose=TRUE): add a removePeaks processing step to the lazy processing @@ -497,8 +423,6 @@

    Data manipulation methods

    The method returns an OnDiskMSnExp object.

    For more details see documentation of the removePeaks method.

    - -
    trimMz

    trimMz(signature(object="OnDiskMSnExp", mzlim="numeric"),...): add a trimMz processing step to the lazy processing queue @@ -506,8 +430,6 @@

    Data manipulation methods

    The method returns an OnDiskMSnExp object.

    For more details see documentation of the trimMz method.

    - -

    Other methods and functions

    @@ -517,15 +439,10 @@

    Other methods and functions

    addition to the standard validObject method, this method reads also all spectra from the original files, applies eventual processing steps and evaluates their validity.

    - -
    as(from, "MSnExp")

    Converts the OnDiskMSnExp object from, to an in-memory MSnExp. Also available as an S3 method as.MSnExp().

    - - -

    Author

    @@ -537,7 +454,6 @@

    See also

    MSnExp, readMSData

    -

    Examples

    ## Get some example mzML files
@@ -1117,9 +1033,9 @@ 
    Examples
    
 #>  Number of spectra: 35 
 #>  MSn retention times: 45:27 - 45:30 minutes
 #> - - - Processing information - - -
-#> Data loaded [Wed May  1 08:22:07 2024] 
-#> Filter: select parent/children scans for 21945 [Wed May  1 08:22:08 2024] 
-#>  MSnbase version: 2.31.0 
+#> Data loaded [Wed May 15 16:29:30 2024] 
+#> Filter: select parent/children scans for 21945 [Wed May 15 16:29:31 2024] 
+#>  MSnbase version: 2.31.1 
 #> - - - Meta data  - - -
 #> phenoData
 #>   rowNames: MS3TMT11.mzML
@@ -1149,9 +1065,9 @@ 
    Examples
    
 #>  Number of spectra: 3 
 #>  MSn retention times: 45:27 - 45:27 minutes
 #> - - - Processing information - - -
-#> Data loaded [Wed May  1 08:22:07 2024] 
-#> Filter: select parent/children scans for 21946 [Wed May  1 08:22:08 2024] 
-#>  MSnbase version: 2.31.0 
+#> Data loaded [Wed May 15 16:29:30 2024] 
+#> Filter: select parent/children scans for 21946 [Wed May 15 16:29:31 2024] 
+#>  MSnbase version: 2.31.1 
 #> - - - Meta data  - - -
 #> phenoData
 #>   rowNames: MS3TMT11.mzML
@@ -1177,22 +1093,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/ProcessingStep-class.html b/reference/ProcessingStep-class.html index 0a12ad00..534fb41f 100644 --- a/reference/ProcessingStep-class.html +++ b/reference/ProcessingStep-class.html @@ -5,8 +5,6 @@ - -
    - - -

    Simple processing step class

    -
    -

    The ProcessingStep class is a simple object to encapsule all relevant information of a data analysis processing step, i.e. the function name and all arguments.

    - -

    Details

    Objects of this class are mainly used to record all possible @@ -95,11 +83,8 @@

    Objects from the Class

    Slots

    FUN:

    The function name to be executed as a character string.

    -
    ARGS:

    A named list with all arguments to the function.

    - -

    Methods and functions

    @@ -109,8 +94,6 @@

    Methods and functions

    ProcessingStep object along with potential additional arguments in ... to the function object@FUN.

    - -

    Extends

    @@ -124,7 +107,6 @@

    Author

    See also

    OnDiskMSnExp

    -

    Examples

    ## Define a simple ProcessingStep
@@ -140,22 +122,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/ReporterIons-class.html b/reference/ReporterIons-class.html index c169f7f1..810c3e10 100644 --- a/reference/ReporterIons-class.html +++ b/reference/ReporterIons-class.html @@ -12,27 +12,19 @@ iTRAQ4: ReporterIon object for the iTRAQ 4-plex set. Load with data(iTRAQ4). - iTRAQ5: ReporterIon object for the iTRAQ 4-plex set plus the isobaric tag. Load with data(iTRAQ5). - TMT6: ReporterIon object for the TMT 6-plex set. Load with data(TMT6). - TMT7: ReporterIon object for the TMT 6-plex set plus the isobaric tag. Load with data(TMT6). - - - '> - -
    - - -

    The "ReporterIons" Class

    -
    -

    The ReporterIons class allows to define a set of isobaric reporter ions that are used for quantification in MSMS @@ -111,23 +95,16 @@

    The "ReporterIons" Class

    are:

    iTRAQ4:

    ReporterIon object for the iTRAQ 4-plex set. Load with data(iTRAQ4).

    -
    iTRAQ5:

    ReporterIon object for the iTRAQ 4-plex set plus the isobaric tag. Load with data(iTRAQ5).

    -
    TMT6:

    ReporterIon object for the TMT 6-plex set. Load with data(TMT6).

    -
    TMT7:

    ReporterIon object for the TMT 6-plex set plus the isobaric tag. Load with data(TMT6).

    - -
    - -

    Objects from the Class

    Objects can be created by calls of the form new("ReporterIons", ...).

    @@ -137,39 +114,31 @@

    Slots

    name:

    Object of class "character" to identify the ReporterIons instance.

    -
    reporterNames:

    Object of class "character" naming each individual reporter of the ReporterIons instance. If not provided explicitely, they are names by concatenating the ReporterIons name and the respective MZ values.

    -
    description:

    Object of class "character" to describe the ReporterIons instance.

    -
    mz:

    Object of class "numeric" providing the MZ values of the reporter ions.

    -
    col:

    Object of class "character" providing colours to highlight the reporters on plots.

    -
    width:

    Object of class "numeric" indicating the width around the individual reporter ions MZ values were to search for peaks. This is dependent on the mass spectrometer's resolution and is used for peak picking when quantifying the reporters. See quantify for more details about quantification.

    -
    .__classVersion__:

    Object of class "Versions" indicating the version of the ReporterIons instance. Intended for developer use and debugging.

    - -

    Extends

    @@ -179,48 +148,37 @@

    Extends

    Methods

    show(object)

    Displays object content as text.

    -
    object[]

    Subsets one or several reporter ions of the ReporterIons object and returns a new instance of the same class.

    -
    length(object)

    Returns the number of reporter ions in the instance.

    -
    mz(object, ...)

    Returns the expected mz values of reporter ions. Additional arguments are currently ignored.

    -
    reporterColours(object) or reporterColors(object)

    Returns the colours used to highlight the reporter ions.

    -
    reporterNames(object)

    Returns the name of the individual reporter ions. If not specified or is an incorrect number of names is provided at initialisation, the names are generated automatically by concatenating the instance name and the reporter's MZ values.

    -
    reporterNames(object) <- value

    Sets the reporter names to value, which must be a character of the same length as the number of reporter ions.

    -
    width(object)

    Returns the widths in which the reporter ion peaks are expected.

    -
    names(object)

    Returns the name of the ReporterIons object.

    -
    description(object)

    Returns the description of the ReporterIons object.

    - -

    References

    @@ -249,7 +207,6 @@

    Author

    See also

    TMT6 or iTRAQ4 for readily available examples.

    -

    Examples

    ## Code used for the iTRAQ4 set
@@ -282,22 +239,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/Spectrum-class.html b/reference/Spectrum-class.html index a65c1933..8a28f9ea 100644 --- a/reference/Spectrum-class.html +++ b/reference/Spectrum-class.html @@ -8,8 +8,6 @@ - -
    - - -

    The "Spectrum" Class

    -
    -

    Virtual container for spectrum data common to all different types of spectra. A Spectrum object can not be directly instanciated. Use @@ -83,8 +73,6 @@

    The "Spectrum" Class

    In version 1.19.12, the polarity slot has been added to this class (previously in "Spectrum1").

    - -

    Slots

    msLevel:
    @@ -92,64 +80,50 @@

    Slots

    the MS level: 1 for MS1 level Spectrum1 objects and 2 for MSMSM Spectrum2 objects. Levels > 2 have not been tested and will be handled as MS2 spectra.

    -
    polarity:

    Object of class "integer" indicating the polarity if the ion.

    -
    peaksCount:

    Object of class "integer" indicating the number of MZ peaks.

    -
    rt:

    Object of class "numeric" indicating the retention time (in seconds) for the current ions.

    -
    tic:

    Object of class "numeric" indicating the total ion current, as reported in the original raw data file.

    -
    acquisitionNum:

    Object of class "integer" corresponding to the acquisition number of the current spectrum.

    -
    scanIndex:

    Object of class "integer" indicating the scan index of the current spectrum.

    -
    mz:

    Object of class "numeric" of length equal to the peaks count (see peaksCount slot) indicating the MZ values that have been measured for the current ion.

    -
    intensity:

    Object of class "numeric" of same length as mz indicating the intensity at which each mz datum has been measured.

    -
    centroided:

    Object of class "logical" indicating if instance is centroided ('TRUE') of uncentroided ('FALSE'). Default is NA.

    -
    smoothed:

    Object of class "logical" indicating if instance is smoothed ('TRUE') of unsmoothed ('FALSE'). Default is NA.

    -
    fromFile:

    Object of class "integer" referencing the file the spectrum originates. The file names are stored in the processingData slot of the "MSnExp" or "MSnSet" instance that contains the current "Spectrum" instance.

    -
    .__classVersion__:

    Object of class "Versions" indicating the version of the Spectrum class. Intended for developer use and debugging.

    - -

    Extends

    @@ -160,18 +134,13 @@

    Methods

    acquisitionNum(object)

    Returns the acquisition number of the spectrum as an integer.

    -
    scanIndex(object)

    Returns the scan index of the spectrum as an integer.

    - -
    centroided(object)

    Indicates whether spectrum is centroided (TRUE), in profile mode (FALSE), or unkown (NA).

    - -
    isCentroided(object, k=0.025, qtl=0.9)

    A heuristic assessing if a spectrum is in profile or centroided mode. The @@ -185,141 +154,110 @@

    Methods

    details. It should however be safe to use is at the experiment level, assuming that all MS level have the same mode. See class?MSnExp for an example.

    - - -
    smoothed(object)

    Indicates whether spectrum is smoothed (TRUE) or not (FALSE).

    - -
    centroided(object) <- value

    Sets the centroided status of the spectrum object.

    -
    smoothed(object) <- value

    Sets the smoothed status of the spectrum object.

    -
    fromFile(object)

    Returns the index of the raw data file from which the current instances originates as an integer.

    -
    intensity(object)

    Returns an object of class numeric containing the intensities of the spectrum.

    -
    msLevel(object)

    Returns an MS level of the spectrum as an integer.

    -
    mz(object, ...)

    Returns an object of class numeric containing the MZ value of the spectrum peaks. Additional arguments are currently ignored.

    -
    peaksCount(object)

    Returns the number of peaks (possibly of 0 intensity) as an integer.

    -
    rtime(object, ...)

    Returns the retention time for the spectrum as an integer. Additional arguments are currently ignored.

    -
    ionCount(object)

    Returns the total ion count for the spectrum as a numeric.

    -
    tic(object, ...)

    Returns the total ion current for the spectrum as a numeric. Additional arguments are currently ignored. This is the total ion current as originally reported in the raw data file. To get the current total ion count, use ionCount.

    - %% -------------------------------------------------- %%
    bin

    signature(object = "Spectrum"): Bins Spectrum. See bin documentation for more details and examples.

    -
    clean

    signature(object = "Spectrum"): Removes unused 0 intensity data points. See clean documentation for more details and examples.

    -
    compareSpectra

    signature(x = "Spectrum", y = "Spectrum"): Compares spectra. See compareSpectra documentation for more details and examples.

    -
    estimateNoise

    signature(object = "Spectrum"): Estimates the noise in a profile spectrum. See estimateNoise documentation for more details and examples.

    -
    pickPeaks

    signature(object = "Spectrum"): Performs the peak picking to generate a centroided spectrum. See pickPeaks documentation for more details and examples.

    -
    plot

    signature(x = "Spectrum", y = "missing"): Plots intensity against mz. See plot.Spectrum documentation for more details.

    -
    plot

    signature(x = "Spectrum", y = "Spectrum"): Plots two spectra above/below each other. See plot.Spectrum.Spectrum documentation for more details.

    -
    plot

    signature(x = "Spectrum", y = "character"): Plots an MS2 level spectrum and its highlight the fragmention peaks. See plot.Spectrum.character documentation for more details.

    -
    quantify

    signature(object = "Spectrum"): Quatifies defined peaks in the spectrum. See quantify documentation for more details.

    -
    removePeaks

    signature(object = "Spectrum"): Remove peaks lower that a threshold t. See removePeaks documentation for more details and examples.

    -
    smooth

    signature(x = "Spectrum"): Smooths spectrum. See smooth documentation for more details and examples.

    -
    show

    signature(object = "Spectrum"): Displays object content as text.

    -
    trimMz

    signature(object = "Spectrum"): Trims the MZ range of all the spectra of the MSnExp instance. See trimMz documentation for more details and examples.

    -
    isEmpty

    signature(x = "Spectrum"): Checks if the x is an empty Spectrum.

    - %% -------------------------------------------------- %%
    as

    signature(object = "Spectrum", "data.frame"): Coerces the Spectrum object to a two-column data.frame containing intensities and MZ values.

    - -

    Author

    @@ -334,28 +272,17 @@

    See also

    Instaciable sub-classes "Spectrum1" and "Spectrum2" for MS1 and MS2 spectra.

    -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/Spectrum1-class.html b/reference/Spectrum1-class.html index 1547c2c7..e00647f9 100644 --- a/reference/Spectrum1-class.html +++ b/reference/Spectrum1-class.html @@ -7,8 +7,6 @@ - -
    - - -

    The "Spectrum1" Class for MS1 Spectra

    -
    -

    Spectrum1 extends the "Spectrum" class and introduces an MS1 specific attribute in addition to the slots in @@ -81,8 +71,6 @@

    The "Spectrum1" Class for MS1 Spectra

    created directly but are contained in the assayData slot of an "MSnExp".

    - -

    Slots

    See the "Spectrum" class for inherited slots.

    @@ -98,8 +86,6 @@

    Methods

    methods to process Spectrum1 objects.

    polarity(object)

    Returns the polarity of the spectrum as an integer.

    - -

    Author

    @@ -111,28 +97,17 @@

    See also

    "Spectrum2" for MS2 spectra and "MSnExp" for a full experiment container.

    -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/Spectrum2-class.html b/reference/Spectrum2-class.html index 590ef723..f5a89256 100644 --- a/reference/Spectrum2-class.html +++ b/reference/Spectrum2-class.html @@ -1,6 +1,5 @@ The "Spectrum2" Class for MSn Spectra — Spectrum2-class • MSnbase -
    precScanNum:

    See precAcquisitionNum.

    -
    calculateFragments

    signature(sequence = "character", object = "Spectrum2"): @@ -177,8 +147,6 @@

    Methods

    sequence with the ones observed in a spectrum. See calculateFragments documentation for more details and examples.

    - -

    Author

    @@ -190,28 +158,17 @@

    See also

    "Spectrum1" for MS1 spectra and "MSnExp" for a full experiment container.

    - - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/TMT6.html b/reference/TMT6.html index fbb9b6f6..1d0d23ce 100644 --- a/reference/TMT6.html +++ b/reference/TMT6.html @@ -1,12 +1,10 @@ TMT 6/10-plex sets — TMT6 • MSnbase - -
    - - -

    Adds Identification Data

    -
    -
    - -

    These methods add identification data to a raw MS experiment (an "MSnExp" object) or to quantitative data (an "MSnSet" object). The identification data needs @@ -89,12 +76,8 @@

    Adds Identification Data

    as an arbitrary data.frame. See details in the Methods section.

    - -

    Details

    - -

    The featureData slots in a "MSnExp" or a "MSnSet" instance provides only one row per MS2 spectrum but the identification is not always bijective. Prior to @@ -123,72 +106,48 @@

    Details

    Methods

    - -

    signature(object = "MSnExp", id = "character", ...

    Adds the identification data stored in mzIdentML files to a "MSnExp" instance. The method handles one or multiple mzIdentML files provided via id. id has to be a character vector of valid filenames. See below for additional arguments.

    - -
    signature(object = "MSnExp", id = "mzID", ...)

    Same as above but id is a mzID object generated by mzID::mzID. See below for additional arguments.

    - -
    signature(object = "MSnExp", id = "mzIDCollection", ...)

    Same as above but id is a mzIDCollection object. See below for additional arguments.

    - -
    signature(object = "MSnExp", id = "mzRident", ...

    Same as above but id is a mzRident object generated by mzR::openIdfile. See below for additional arguments.

    - - -
    signature(object = "MSnExp", id = "data.frame", ...

    Same as above but id could be a data.frame. See below for additional arguments.

    - -
    signature(object = "MSnSet", id = "character", ...)

    Adds the identification data stored in mzIdentML files to an "MSnSet" instance. The method handles one or multiple mzIdentML files provided via id. id has to be a character vector of valid filenames. See below for additional arguments.

    - -
    signature(object = "MSnSet", id = "mzID", ...)

    Same as above but id is a mzID object. See below for additional arguments.

    - -
    signature(object = "MSnSet", id = "mzIDCollection", ...)

    Same as above but id is a mzIDCollection object. See below for additional arguments.

    - -
    signature(object = "MSnSet", id = "data.frame", ...)

    Same as above but id is a data.frame. See below for additional arguments.

    - - -

    The methods above take the following additional argument. These need to be set when adding identification data as a data.frame. In all other cases, the defaults are set automatically.

    -

    fcol
    -

    The matching between the features (raw spectra or quantiative features) and identification results is done by matching columns in the featue data (the featureData slot) and the @@ -199,54 +158,39 @@

    Methods

    "acquisition.num". Values need to be provided when id is a data.frame.

    - -
    icol
    -

    The default values for the spectrum file and acquisition numbers in the identification data (the id argument) are "spectrumFile" and "acquisitionNum". Values need to - be provided when id is a data.frame.

    + be provided when id is a data.frame.

    - -
    acc
    -

    The protein (group) accession number or identifier. Defaults are "DatabaseAccess" when passing filenames or mzRident objects and "accession" when passing mzID or mzIDCollection objects. A value needs to be provided when id is a data.frame.

    - -
    desc
    -

    The protein (group) description. Defaults are "DatabaseDescription" when passing filenames or mzRident objects and "description" when passing mzID or mzIDCollection objects. A value needs to be provided when id is a data.frame.

    - -
    pepseq
    -

    The peptide sequence variable name. Defaults are "sequence" when passing filenames or mzRident objects and "pepseq" when passing mzID or mzIDCollection objects. A value needs to be provided when id is a data.frame.

    - -
    key
    -

    The key to be used when the identification data need to be reduced (see details section). Defaults are "spectrumID" when passing filenames or mzRident objects and @@ -254,11 +198,8 @@

    Methods

    mzIDCollection objects. A value needs to be provided when id is a data.frame.

    - -
    decoy
    -

    The feature variable used to define whether the PSM was matched in the decoy of regular fasta database for PSM filtering. Defaults are "isDecoy" when passing filenames or mzRident @@ -267,36 +208,25 @@

    Methods

    id is a data.frame. See filterIdentificationDataFrame for details.

    - -
    rank
    -

    The feature variable used to defined the rank of the PSM for filtering. Defaults is "rank". A value needs to be provided when id is a data.frame. See filterIdentificationDataFrame for details.

    - -
    accession
    -

    The feature variable used to defined the protein (groupo) accession or identifier for PSM filterin. Defaults is to use the same value as acc . A value needs to be provided when id is a data.frame. See - filterIdentificationDataFrame for details.

    + filterIdentificationDataFrame for details.

    - -
    verbose

    A logical defining whether to print out messages or not. Default is to use the session-wide open from isMSnbaseVerbose.

    - - -

    Author

    @@ -305,14 +235,12 @@

    Author

    See also

    -

    filterIdentificationDataFrame for the function that filters identification data, readMzIdData to read the identification data as a unfiltered data.frame and reduce,data.frame-method to reduce it to a data.frame that contains only unique PSMs per row.

    -

    Examples

    ## find path to a mzXML file
@@ -389,22 +317,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/aggvar.html b/reference/aggvar.html index b3b66989..925ec163 100644 --- a/reference/aggvar.html +++ b/reference/aggvar.html @@ -5,8 +5,6 @@ - -
    - - -
    @@ -71,38 +63,28 @@

    Identify aggregation outliers

    Source: R/combineFeatures.R
    -

    This function evaluates the variability within all protein group of an MSnSet. If a protein group is composed only of a single feature, NA is returned.

    - 
    aggvar(object, groupBy, fun)
    -

    Arguments

    object

    An object of class MSnSet.

    - -
    groupBy

    A character containing the protein grouping feature variable name.

    - -
    fun

    A function the summarise the distance between features within protein groups, typically max or mean.median.

    -

    Value

    - -

    A matrix providing the number of features per protein group (nb_feats column) and the aggregation summarising distance (agg_dist column).

    @@ -127,7 +109,6 @@

    See also

    Author

    Laurent Gatto

    -

    Examples

    library("pRolocdata")
@@ -148,22 +129,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/averageMSnSet.html b/reference/averageMSnSet.html index 0de02e1e..e5d83ecf 100644 --- a/reference/averageMSnSet.html +++ b/reference/averageMSnSet.html @@ -5,8 +5,6 @@ - -
    - - -
    @@ -71,29 +63,22 @@

    Generate an average MSnSet

    Source: R/averageMSnSet.R
    -

    Given a list of MSnSet instances, typically representing replicated experiments, the function returns an average MSnSet.

    - 
    averageMSnSet(x, avg = function(x) mean(x, na.rm = TRUE), disp = npcv)
    -

    Arguments

    x

    A list of valid MSnSet instances to be averaged.

    - -
    avg

    The averaging function. Default is the mean after removing missing values, as computed by function(x) mean(x, na.rm = TRUE).

    - -
    disp

    The disperion function. Default is an non-parametric coefficient of variation that replaces the standard deviation by @@ -102,12 +87,9 @@

    Arguments

    details. Note that the mad of a single value is 0 (as opposed to NA for the standard deviation, see example below).

    -

    Value

    - -

    A new average MSnSet.

    @@ -141,7 +123,6 @@

    See also

    Author

    Laurent Gatto

    -

    Examples

    library("pRolocdata")
@@ -205,7 +186,7 @@ 
    Examples
    
 #> Loading required package: cluster
 #> Loading required package: BiocParallel
 #> 
-#> This is pRoloc version 1.43.2 
+#> This is pRoloc version 1.44.0 
 #>   Visit https://lgatto.github.io/pRoloc/ to get started.
 setStockcol(paste0(getStockcol(), "AA"))
 plot2D(avg, cex = 7.7 * disp)
@@ -219,22 +200,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/bin-methods.html b/reference/bin-methods.html index 62f0198b..718284dc 100644 --- a/reference/bin-methods.html +++ b/reference/bin-methods.html @@ -5,8 +5,6 @@ - -
    - - -

    Bin 'MSnExp' or 'Spectrum' instances

    -
    -

    This method aggregates individual spectra (Spectrum instances) or whole experiments (MSnExp instances) into discrete bins. All intensity values which belong to the same bin are summed together.

    - -

    Methods

    signature(object = "MSnExp", binSize = "numeric", verbose = @@ -88,8 +76,6 @@

    Methods

    (in Dalton, default is 1). Displays a control bar if verbose set to TRUE (default). Returns a binned MSnExp instance.

    - -
    signature(object = "Spectrum", binSize = "numeric", breaks = "numeric", msLevel. = "numeric")

    Bin the @@ -99,10 +85,8 @@

    Methods

    specify the breakpoints between m/z bins. msLevel. defines the level of the spectrum, and if msLevel(object) != msLevel., cleaning is ignored. Only relevant when called - from OnDiskMSnExp and is only relevant for developers.

    + from OnDiskMSnExp and is only relevant for developers.

    Returns a binned Spectrum instance.

    - -

    Author

    @@ -114,7 +98,6 @@

    See also

    removePeaks and trimMz for other spectra processing methods.

    -

    Examples

    s <- new("Spectrum2", mz=1:10, intensity=1:10)
@@ -133,7 +116,7 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> Updated from version 0.3.0 to 0.3.1 [Fri Jul  8 20:23:25 2016] 
-#> Spectra binned: Wed May  1 08:22:18 2024 
+#> Spectra binned: Wed May 15 16:29:41 2024 
 #>  MSnbase version: 1.1.22
    @@ -142,22 +125,12 @@

    Examples

    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/calculateFragments-methods.html b/reference/calculateFragments-methods.html index 1d74a981..c12145dd 100644 --- a/reference/calculateFragments-methods.html +++ b/reference/calculateFragments-methods.html @@ -4,8 +4,6 @@ - -
    - - -

    Calculate ions produced by fragmentation.

    -
    -

    These method calculates a-, b-, c-, x-, y- and z-ions produced by fragmentation.

    - -

    Arguments

    sequence

    character, peptide sequence.

    -
    object

    Object of class "Spectrum2" or "missing" .

    -
    tolerance

    numeric tolerance between the theoretical and measured MZ values (only available if object is not missing).

    -
    method

    method used for for duplicated matches. Choose "highest" or "closest" to select the peak with the highest intensity respectively the closest MZ in the tolerance range. If "all" is given all possible matches in the tolerance range are reported (only available if object is not missing).

    -
    type

    character vector of target ions; possible values: c("a", "b", "c", "x", "y", "z"); default: type=c("b", "y").

    -
    z

    numeric desired charge state; default z=1.

    -
    modifications

    named numeric vector of used modifications. The name must correspond to the one-letter-code of the modified amino acid and @@ -112,7 +94,6 @@

    Arguments

    Carbamidomethyl modifications=c(C=57.02146). Use Nterm or Cterm as names for modifications that should be added to the amino respectively carboxyl-terminus.

    -
    neutralLoss

    list, it has to have two named elments, namely water and ammonia that contain a @@ -125,11 +106,9 @@

    Arguments

    correct list. It has two arguments disableWaterLoss and disableAmmoniaLoss to remove single neutral loss options. See the example section for use cases.

    -
    verbose

    logical if TRUE (default) the used modifications are printed.

    -

    Methods

    @@ -137,7 +116,6 @@

    Methods

    Calculates the theoretical fragments for a peptide sequence. Returns a data.frame with the columns c("mz", "ion", "type", "pos", "z", "seq").

    -
    signature(sequence = "character", object = "Spectrum2", ...)

    Calculates and matches the theoretical fragments for a peptide sequence and a "Spectrum2" object. @@ -159,14 +137,11 @@

    Methods

    is a column error that contains the difference between the observed MZ (from the spectrum) to the theoretical fragment MZ.

    - -

    Author

    Sebastian Gibb <mail@sebastiangibb.de>

    -

    Examples

    ## find path to a mzXML file
@@ -783,22 +758,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/chromatogram-MSnExp-method.html b/reference/chromatogram-MSnExp-method.html index cb93ab9f..c47fc276 100644 --- a/reference/chromatogram-MSnExp-method.html +++ b/reference/chromatogram-MSnExp-method.html @@ -7,8 +7,6 @@ - -
    - - -
    @@ -73,7 +65,6 @@

    Extract chromatogram object(s)

    Source: R/methods-MSnExp.R
    -

    The chromatogram method extracts chromatogram(s) from an MSnExp or OnDiskMSnExp object. @@ -81,7 +72,6 @@

    Extract chromatogram object(s)

    (TIC), a base peak chromatogram (BPC) or an extracted ion chromatogram (XIC) extracted from each sample/file.

    - 
    # S4 method for class 'MSnExp'
 chromatogram(
@@ -94,23 +84,18 @@ 
    Extract chromatogram object(s)
    
   BPPARAM = bpparam()
 )
    -

    Arguments

    object

    For chromatogram: a MSnExp or OnDiskMSnExp object from which the chromatogram should be extracted.

    - -
    rt

    A numeric(2) or two-column matrix defining the lower and upper boundary for the retention time range/window(s) for the chromatogram(s). If a matrix is provided, a chromatogram is extracted for each row. If not specified, a chromatogram representing the full retention time range is extracted. See examples below for details.

    - -
    mz

    A numeric(2) or two-column matrix defining the mass-to-charge (mz) range(s) for the chromatogram(s). For each @@ -118,35 +103,24 @@

    Arguments

    aggregated to result in the intensity value for the spectrum/retention time. If not specified, the full mz range is considered. See examples below for details.

    - -
    aggregationFun

    character defining the function to be used for intensity value aggregation along the mz dimension. Allowed values are "sum" (TIC), "max" (BPC), "min" and "mean".

    - -
    missing

    numeric(1) allowing to specify the intensity value for if for a given retention time (spectrum) no signal was measured within the mz range. Defaults to NA_real_.

    - -
    msLevel

    integer specifying the MS level from which the chromatogram should be extracted. Defaults to msLevel = 1L.

    - -
    BPPARAM

    Parallelisation backend to be used, which will depend on the architecture. Default is BiocParallel::bpparam().

    -

    Value

    - -

    chromatogram returns a MChromatograms object with the number of columns corresponding to the number of files in object and number of rows the number of specified ranges (i.e. @@ -189,7 +163,6 @@

    See also

    Author

    Johannes Rainer

    -

    Examples

    ## Read a test data file.
@@ -286,22 +259,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/clean-methods.html b/reference/clean-methods.html index 814b8845..d23aadd6 100644 --- a/reference/clean-methods.html +++ b/reference/clean-methods.html @@ -11,8 +11,6 @@ - -
    - - -

    Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances

    -
    -

    This method cleans out individual spectra (Spectrum instances), chromatograms (Chromatogram instances) @@ -89,8 +79,6 @@

    Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances

    only one 0-intensity value, it is retained. An illustrative example is shown below.

    - -

    Methods

    signature(object = "MSnExp", all = "logical", verbose = @@ -98,8 +86,6 @@

    Methods

    Cleans all spectra in MSnExp object. Displays a control bar if verbose set to TRUE (default). Returns a cleaned MSnExp instance.

    - -
    signature(object = "Spectrum", all = "logical", msLevel. = "numeric")

    Cleans the Spectrum @@ -108,16 +94,12 @@

    Methods

    level of the spectrum, and if msLevel(object) != msLevel., cleaning is ignored. Only relevant when called from OnDiskMSnExp and is only relevant for developers.

    - -
    signature(object = "Chromatogram", all = "logical", na.rm = "logical")

    Cleans the Chromatogram instance and returns a cleaned Chromatogram object. If na.rm is TRUE (default is FALSE) all NA intensities are removed before cleaning the chromatogram.

    - -

    Author

    @@ -128,7 +110,6 @@

    See also

    removePeaks and trimMz for other spectra processing methods.

    -

    Examples

    int <- c(1,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0)
@@ -161,7 +142,7 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> Updated from version 0.3.0 to 0.3.1 [Fri Jul  8 20:23:25 2016] 
-#> Spectra cleaned: Wed May  1 08:22:29 2024 
+#> Spectra cleaned: Wed May 15 16:29:53 2024 
 #>  MSnbase version: 1.1.22 
 
 ## Create a simple Chromatogram object
@@ -192,22 +173,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/combineFeatures.html b/reference/combineFeatures.html index 1706519d..87928177 100644 --- a/reference/combineFeatures.html +++ b/reference/combineFeatures.html @@ -1,6 +1,5 @@ Combines features in an MSnSet object — combineFeatures • MSnbase combineSpectra( @@ -103,49 +93,33 @@

    Combine Spectra

    # S4 method for class 'MSpectra' combineSpectra(object, fcol, method = meanMzInts, fun, ...)
    -

    Arguments

    object

    A MSnExp or MSpectra

    - -
    fcol

    For MSpectra objects: mcols column name to be used to define the sets of spectra to be combined. If missing, all spectra are considered to be one set. For MSnExp/OnDiskMSnExp objects: column in fData(object) defining which spectra to combine. See examples below for more details.

    - -
    method

    function to be used to combine the spectra by fcol. Has to be a function that takes a list of spectra as input and returns a single Spectrum. See meanMzInts() for details.

    - -
    ...

    additional arguments for fun.

    - -
    BPPARAM

    For MSnExp/OnDiskMSnExp objects: parallel processing setup to perform per-file parallel spectra combining. See bpparam() for more details.

    - -
    fun

    Deprecated use method instead.

    -

    Value

    - -

    A MSpectra or MSnExp object with combined spectra. Metadata (mcols) and all spectrum attributes other than mz and intensity

    - -

    are taken from the first Spectrum in each set.

    @@ -156,7 +130,6 @@

    See also

    Author

    Johannes Rainer, Laurent Gatto

    -

    Examples

    
@@ -268,22 +241,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/combineSpectraMovingWindow.html b/reference/combineSpectraMovingWindow.html index 0dd24c70..2edd80c7 100644 --- a/reference/combineSpectraMovingWindow.html +++ b/reference/combineSpectraMovingWindow.html @@ -10,8 +10,6 @@ - -
    - - -
    @@ -76,7 +68,6 @@

    Combine signal from consecutive spectra of LCMS experiments

    Source: R/functions-MSnExp.R
    -

    combineSpectraMovingWindow combines signal from consecutive spectra within a file. The resulting MSnExp has the same total number of spectra than the @@ -87,7 +78,6 @@

    Combine signal from consecutive spectra of LCMS experiments

    Note that the function returns always a MSnExp object, even if x was an OnDiskMSnExp object.

    - 
    combineSpectraMovingWindow(
   x,
@@ -100,32 +90,23 @@ 
    Combine signal from consecutive spectra of LCMS experiments
    
   BPPARAM = bpparam()
 )
    -

    Arguments

    x

    MSnExp or OnDiskMSnExp object.

    - -
    halfWindowSize

    integer(1) with the half window size for the moving window.

    - -
    intensityFun

    function to aggregate the intensity values per m/z group. Should be a function or the name of a function. The function is expected to return a numeric(1).

    - -
    mzd

    numeric(1) defining the maximal m/z difference below which mass peaks are considered to represent the same ion/mass peak. Intensity values for such grouped mass peaks are aggregated. If not specified this value is estimated from the distribution of differences of m/z values from the provided spectra (see details).

    - -
    timeDomain

    logical(1) whether definition of the m/z values to be combined into one m/z is performed on m/z values @@ -134,29 +115,20 @@

    Arguments

    on the time domain (see details). Note that a pre-defined mzd should also be estimated on the square root of m/z values if timeDomain = TRUE.

    - -
    weighted

    logical(1) whether m/z values per m/z group should be aggregated with an intensity-weighted mean. The default is to report the mean m/z.

    - -
    ppm

    numeric(1) to define an m/z relative deviation. Note that if only ppm should be considered but not mzd, mzd should be set to 0 (i.e. mzd = 0). This parameter is directly passed to meanMzInts().

    - -
    BPPARAM

    parallel processing settings.

    -

    Value

    - -

    MSnExp with the same number of spectra than x.

    @@ -204,7 +176,6 @@

    See also

    Author

    Johannes Rainer, Sigurdur Smarason

    -

    Examples

    
@@ -267,22 +238,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/commonFeatureNames.html b/reference/commonFeatureNames.html index d2ab49fa..09be86db 100644 --- a/reference/commonFeatureNames.html +++ b/reference/commonFeatureNames.html @@ -3,8 +3,6 @@ - -
    - - -
    @@ -69,45 +61,34 @@

    Keep only common feature names

    Source: R/functions-MSnSet.R
    -

    Subsets MSnSet instances to their common feature names.

    - 
    commonFeatureNames(x, y)
    -

    Arguments

    x

    An instance of class MSnSet or a list or MSnSetList with at least 2 MSnSet objects.

    - -
    y

    An instance of class MSnSet. Ignored if x is a list/MSnSetList.

    -

    Value

    - -

    An linkS4class{MSnSetList} composed of the input MSnSet containing only common features in the same order. The names of the output are either the names of the x and y input variables or the names of x

    - -

    if a list is provided.

    Author

    Laurent Gatto

    -

    Examples

    library("pRolocdata")
@@ -136,22 +117,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/compareMSnSets.html b/reference/compareMSnSets.html index 46f1453f..5cde2a2a 100644 --- a/reference/compareMSnSets.html +++ b/reference/compareMSnSets.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,70 +62,45 @@

    Compare two MSnSets

    Source: R/utils.R
    -

    Compares two MSnSet instances. The qual and processingData slots are generally omitted.

    - 
    compareMSnSets(x, y, qual = FALSE, proc = FALSE)
    -

    Arguments

    x

    First MSnSet

    - -
    y

    Second MSnSet

    - -
    qual

    Should the qual slots be compared? Default is FALSE.

    - -
    proc

    Should the processingData slots be compared? Default is FALSE.

    -

    Value

    - -

    A logical

    - -

    Author

    Laurent Gatto

    -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/compareSpectra-methods.html b/reference/compareSpectra-methods.html index bb14a736..36498883 100644 --- a/reference/compareSpectra-methods.html +++ b/reference/compareSpectra-methods.html @@ -19,8 +19,6 @@ - -
    - - -

    Compare Spectra of an 'MSnExp' or 'Spectrum' instances

    -
    -

    This method compares spectra (Spectrum instances) pairwise or all spectra of an experiment (MSnExp instances). Currently @@ -105,8 +95,6 @@

    Compare Spectra of an 'MSnExp' or 'Spectrum' instances

    and ... as third argument. The function must return a single numeric value. See the example section.

    - -

    Methods

    signature(x = "MSnExp", y = "missing", fun = @@ -115,17 +103,11 @@

    Methods

    object. The ... arguments are passed to the internal functions. Returns a matrix of dimension length(x) by length(x).

    - - -
    signature(x = "Spectrum", y = "Spectrum", fun = "character", ...)

    Compares two Spectrum objects. See the above explanation for fun and .... Returns a single numeric value.

    - - -

    Author

    @@ -151,7 +133,6 @@

    References

    Proteomics, 7: 655-667. doi: https://doi.org/10.1002/pmic.200600625

    -

    Examples

    s1 <- new("Spectrum2", mz=1:10, intensity=1:10)
@@ -189,22 +170,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/consensusSpectrum.html b/reference/consensusSpectrum.html index b3e49e5a..2d758fb7 100644 --- a/reference/consensusSpectrum.html +++ b/reference/consensusSpectrum.html @@ -5,8 +5,6 @@ - -
    - - -
    @@ -71,13 +63,11 @@

    Combine spectra to a consensus spectrum

    Source: R/functions-Spectrum.R
    -

    consensusSpectrum takes a list of spectra and combines them to a consensus spectrum containing mass peaks that are present in a user definable proportion of spectra.

    - 
    consensusSpectrum(
   x,
@@ -90,14 +80,11 @@ 
    Combine spectra to a consensus spectrum
    
   ...
 )
    -

    Arguments

    x

    list of Spectrum objects (either Spectrum1 or Spectrum2).

    - -
    mzd

    numeric(1) defining the maximal m/z difference below which mass peaks are grouped in to the same final mass peak (see details for @@ -105,42 +92,29 @@

    Arguments

    this value from the distribution of differences of m/z values from the spectra. See also parameter ppm below for the definition of an m/z dependent peak grouping.

    - -
    minProp

    numeric(1) defining the minimal proportion of spectra in which a mass peak has to be present in order to include it in the final consensus spectrum. Should be a number between 0 and 1 (present in all spectra).

    - -
    intensityFun

    function (or name of a function) to be used to define the intensity of the aggregated peak. By default the median signal for a mass peak is reported.

    - -
    mzFun

    function (or name of a function) to be used to define the intensity of the aggregated peak. By default the median m/z is reported. Note that setting weighted = TRUE overrides this parameter.

    - -
    ppm

    numeric(1) allowing to perform a m/z dependent grouping of mass peaks. See details for more information.

    - -
    weighted

    logical(1) whether the m/z of the aggregated peak represents the intensity-weighted average of the m/z values of all peaks of the peak group. If FALSE (the default), the m/z of the peak is calculated with mzFun.

    - -
    ...

    additional arguments to be passed to intensityFun.

    -

    Details

    @@ -157,14 +131,13 @@

    Details

    See also

    -

    Other spectra combination functions: +

    Other spectra combination functions: meanMzInts()

    Author

    Johannes Rainer

    -

    Examples

    library(MSnbase)
@@ -213,22 +186,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/defunct.html b/reference/defunct.html index e066539d..0e891e56 100644 --- a/reference/defunct.html +++ b/reference/defunct.html @@ -8,8 +8,6 @@ - -
    - - -

    MSnbase Deprecated and Defunct

    -
    -

    The function, class, or data object you have asked for has been deprecated or made defunct.

    @@ -83,30 +73,17 @@

    MSnbase Deprecated and Defunct

    writeMzTabData, makeMTD, makePEP, makePRT, NAnnotatedDataFrame class.

    - - -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/estimateMzResolution.html b/reference/estimateMzResolution.html index 026df61e..0a8081d3 100644 --- a/reference/estimateMzResolution.html +++ b/reference/estimateMzResolution.html @@ -6,8 +6,6 @@ - -
    - - -
    @@ -72,14 +64,12 @@

    Estimate the m/z resolution of a spectrum

    Source: R/methods-MSnExp.R, R/methods-Spectrum.R
    -

    estimateMzResolution estimates the m/z resolution of a profile-mode Spectrum (or of all spectra in an MSnExp or OnDiskMSnExp object. The m/z resolution is defined as the most frequent difference between a spectrum's m/z values.

    - 
    # S4 method for class 'MSnExp'
 estimateMzResolution(object, ...)
@@ -87,21 +77,15 @@ 
    Estimate the m/z resolution of a spectrum
    
 # S4 method for class 'Spectrum'
 estimateMzResolution(object, ...)
    -

    Arguments

    object

    either a Spectrum, MSnExp or OnDiskMSnExp object.

    - -
    ...

    currently not used.

    -

    Value

    - -

    numeric(1) with the m/z resolution. If called on a MSnExp or OnDiskMSnExp a list of m/z resolutions are returned (one for each spectrum).

    @@ -118,7 +102,6 @@

    Note

    Author

    Johannes Rainer

    -

    Examples

    
@@ -150,22 +133,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/estimateMzScattering.html b/reference/estimateMzScattering.html index a3c2bffb..784c3663 100644 --- a/reference/estimateMzScattering.html +++ b/reference/estimateMzScattering.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,33 +62,25 @@

    Estimate m/z scattering in consecutive scans

    Source: R/functions-MSnExp.R
    -

    Estimate scattering of m/z values (due to technical, instrument specific noise) for the same ion in consecutive scans of a LCMS experiment.

    - 
    estimateMzScattering(x, halfWindowSize = 1L, timeDomain = FALSE)
    -

    Arguments

    x

    MSnExp or OnDiskMSnExp object.

    - -
    halfWindowSize

    integer(1) defining the half window size for the moving window to combine consecutive spectra.

    - -
    timeDomain

    logical(1) whether m/z scattering should be estimated on mz (timeDomain = FALSE) or sqrt(mz) (timeDomain = TRUE) values. See combineSpectraMovingWindow() for details on this parameter.

    -

    Details

    @@ -123,7 +107,6 @@

    See also

    Author

    Johannes Rainer

    -

    Examples

    
@@ -157,22 +140,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/estimateNoise-method.html b/reference/estimateNoise-method.html index a7916d30..2c1d2562 100644 --- a/reference/estimateNoise-method.html +++ b/reference/estimateNoise-method.html @@ -9,8 +9,6 @@ - -
    - - -

    Noise Estimation for 'Spectrum' instances

    -
    -

    This method performs a noise estimation on individual spectra (Spectrum instances). @@ -85,8 +75,6 @@

    Noise Estimation for 'Spectrum' instances

    as implemented in the MALDIquant::detectPeaks and MALDIquant::estimateNoise functions respectively.

    - -

    Methods

    signature(object = "Spectrum", method = "character", ...)
    @@ -100,12 +88,8 @@

    Methods

    details. This method returns a two-column matrix with the m/z and intensity values in the first and the second column.

    - -
    signature(object = "MSnExp", method = "character", ...)

    Estimates noise for all spectra in object.

    - -

    Author

    @@ -123,7 +107,6 @@

    References

    Bioinformatics 28: 2270-2271. http://strimmerlab.org/software/maldiquant/

    -

    Examples

    sp1 <- new("Spectrum1",
@@ -150,22 +133,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/extractPrecSpectra-methods.html b/reference/extractPrecSpectra-methods.html index 22a853a2..5643cf09 100644 --- a/reference/extractPrecSpectra-methods.html +++ b/reference/extractPrecSpectra-methods.html @@ -7,8 +7,6 @@ - -
    - - -

    Extracts precursor-specific spectra from an 'MSnExp' object

    -
    -

    Extracts the MSMS spectra that originate from the precursor(s) having the same MZ value as defined in theprec argument.

    @@ -81,21 +71,16 @@

    Extracts precursor-specific spectra from an 'MSnExp' object

    in prec are absent in the experiment precursor MZ values (i.e in precursorMz(object)).

    - -

    Methods

    signature(object = "MSnExp", prec = "numeric")

    Returns an "MSnExp" containing MSMS spectra whose precursor MZ values are in prec.

    - -

    Author

    Laurent Gatto <lg390@cam.ac.uk>

    -

    Examples

    file <- dir(system.file(package="MSnbase",dir="extdata"),
@@ -111,9 +96,9 @@ 
    Examples
    
 #> 645.3741 645.3741 
 processingData(bb)
 #> - - - Processing information - - -
-#> Data loaded: Wed May  1 08:22:46 2024 
-#> 1 (2) precursors (spectra) extracted: Wed May  1 08:22:46 2024 
-#>  MSnbase version: 2.31.0 
+#> Data loaded: Wed May 15 16:30:13 2024 
+#> 1 (2) precursors (spectra) extracted: Wed May 15 16:30:13 2024 
+#>  MSnbase version: 2.31.1
    @@ -121,22 +106,12 @@

    Examples

    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/extractSpectraData.html b/reference/extractSpectraData.html index fa7d0cbb..caed6fea 100644 --- a/reference/extractSpectraData.html +++ b/reference/extractSpectraData.html @@ -9,8 +9,6 @@ - -
    - - -
    @@ -75,7 +67,6 @@

    Extract data from MSnbase objects for use in Spectra

    Source: R/functions-MSpectra.R
    -

    extractSpectraData extracts the spectra data (m/z and intensity values including metadata) from MSnExp, OnDiskMSnExp, @@ -85,22 +76,17 @@

    Extract data from MSnbase objects for use in Spectra

    to convert data from the old MSnbase package to the newer Spectra package.

    - 
    extractSpectraData(x)
    -

    Arguments

    x

    a list of Spectrum objects or an object extending MSnExp or a MSpectra object.

    -

    Value

    - -

    DataFrame() with the full spectrum data that can be passed to the Spectra::Spectra() function to create a Spectra object.

    @@ -108,7 +94,6 @@

    Value

    Author

    Johannes Rainer

    -

    Examples

    
@@ -263,22 +248,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/fData-utils.html b/reference/fData-utils.html index 37fdbc22..6be36b63 100644 --- a/reference/fData-utils.html +++ b/reference/fData-utils.html @@ -8,8 +8,6 @@ - -
    - - -
    @@ -74,7 +66,6 @@

    Expand or merge feature variables

    Source: R/fData-utils.R
    -

    The expandFeatureVars and mergeFeatureVars respectively expand and merge groups of feature variables. Using these functions, a @@ -83,46 +74,34 @@

    Expand or merge feature variables

    expanded into single feature columns. The original feature variables are removed.

    - 
    expandFeatureVars(x, fcol, prefix)
 
 mergeFeatureVars(x, fcol, fcol2)
    -

    Arguments

    x

    An object of class MSnSet.

    - -
    fcol

    A character() of feature variables to expand (for expandFeatureVars) or merge (for mergeFeatureVars).

    - -
    prefix

    A character(1) to use as prefix to the new feature variables. If missing (default), then fcol is used instead. If NULL, then no prefix is used.

    - -
    fcol2

    A character(1) defining the name of the new feature variable.

    -

    Value

    - -

    An MSnSet for expanded (merged) feature variables.

    Author

    Laurent Gatto

    -

    Examples

    library("pRolocdata")
@@ -222,22 +201,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/factorsAsStrings.html b/reference/factorsAsStrings.html index b594b47b..b206aea2 100644 --- a/reference/factorsAsStrings.html +++ b/reference/factorsAsStrings.html @@ -5,8 +5,6 @@ - -
    - - -
    @@ -71,27 +63,21 @@

    Converts factors to strings

    Source: R/utils.R
    -

    This function produces the opposite as the stringsAsFactors argument in the data.frame or read.table functions; it converts factors columns to characters.

    - 
    factorsAsStrings(x)
    -

    Arguments

    x

    A data.frame

    -

    Value

    - -

    A data.frame where factors are converted to characters.

    @@ -99,7 +85,6 @@

    Value

    Author

    Laurent Gatto

    -

    Examples

    data(iris)
@@ -124,22 +109,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/featureCV.html b/reference/featureCV.html index cd5f400f..26a1062e 100644 --- a/reference/featureCV.html +++ b/reference/featureCV.html @@ -7,8 +7,6 @@ - -
    - - -
    @@ -73,7 +65,6 @@

    Calculates coeffivient of variation for features

    Source: R/functions-MSnSet.R
    -

    This function calculates the column-wise coefficient of variation (CV), i.e. the ration between the standard deviation and the @@ -81,44 +72,31 @@

    Calculates coeffivient of variation for features

    for the groups of features defined by groupBy. For groups defined by single features, NA is returned.

    - 
    featureCV(x, groupBy, na.rm = TRUE, norm = "none", suffix = NULL)
    -

    Arguments

    x

    An instance of class MSnSet.

    - -
    groupBy

    An object of class factor defining how to summarise the features.

    - -
    na.rm

    A logical(1) defining whether missing values should be removed.

    - -
    norm

    One of normalisation methods applied prior to CV calculation. See normalise() for more details. Here, the default is 'none', i.e. no normalisation.

    - -
    suffix

    A character(1) to be used to name the new CV columns. Default is NULL to ignore this. This argument should be set when CV values are already present in the MSnSet feature variables.

    -

    Value

    - -

    A matrix of dimensions length(levels(groupBy)) by ncol(x) with the respecive CVs. The column names are formed by pasting CV. and the sample names of object x, possibly @@ -132,7 +110,6 @@

    See also

    Author

    Laurent Gatto and Sebastian Gibb

    -

    Examples

    data(msnset)
@@ -153,22 +130,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/fillUp.html b/reference/fillUp.html index fe659a6d..31596bd0 100644 --- a/reference/fillUp.html +++ b/reference/fillUp.html @@ -8,8 +8,6 @@ - -
    - - -

    Fills up a vector

    -
    -

    This function replaces all the empty characters "" and/or NAs with the value of the closest preceding the preceding @@ -83,31 +73,23 @@

    Fills up a vector

    a set of partially identical rows are explicitly populated and the following are empty.

    - 
    fillUp(x)
    -

    Arguments

    x

    a vector.

    -

    Value

    - -

    A vector as x with all empty characters "" and NA

    - -

    values replaced by the preceding non-NA/"" value.

    Author

    Laurent Gatto <lg390@cam.ac.uk>

    -

    Examples

    d <- data.frame(protein=c("Prot1","","","Prot2","",""),
@@ -147,22 +129,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/filterIdentificationDataFrame.html b/reference/filterIdentificationDataFrame.html index 20504aee..773219b3 100644 --- a/reference/filterIdentificationDataFrame.html +++ b/reference/filterIdentificationDataFrame.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,12 +62,10 @@

    Filter out unreliable PSMs.

    Source: R/functions-addIdentificationData.R
    -

    A function to filter out PSMs matching to the decoy database, of rank greater than one and matching non-proteotypic peptides.

    - 
    filterIdentificationDataFrame(
   x,
@@ -86,46 +76,32 @@ 
    Filter out unreliable PSMs.
    
   verbose = isMSnbaseVerbose()
 )
    -

    Arguments

    x

    A data.frame containing PSMs.

    - -
    decoy

    The column name defining whether entries match the decoy database. Default is "isDecoy". The column should be a logical and only PSMs holding a FALSE are retained. Ignored is set to NULL.

    - -
    rank

    The column name holding the rank of the PSM. Default is "rank". This column should be a numeric and only PSMs having rank equal to 1 are retained. Ignored is set to NULL.

    - -
    accession

    The column name holding the protein (groups) accession. Default is "DatabaseAccess". Ignored is set to NULL.

    - -
    spectrumID

    The name of the spectrum identifier column. Default is spectrumID.

    - -
    verbose

    A logical verbosity flag. Default is to take isMSnbaseVerbose().

    -

    Value

    - -

    A new data.frame with filtered out peptides and with the same columns as the input x.

    @@ -140,28 +116,17 @@

    Details

    Author

    Laurent Gatto

    -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/formatRt.html b/reference/formatRt.html index 30e9b465..756155c1 100644 --- a/reference/formatRt.html +++ b/reference/formatRt.html @@ -5,8 +5,6 @@ - -
    - - -
    @@ -71,35 +63,28 @@

    Format Retention Time

    Source: R/utils.R
    -

    This function is used to convert retention times. Conversion is seconds to/from the more human friendly format "mm:sec". The implementation is from MsCoreUtils::formatRt().

    - 
    formatRt(rt)
    -

    Arguments

    rt

    retention time in seconds (numeric) or "mm:sec" (character).

    -

    Value

    - -

    A vector of same length as rt.

    Author

    Laurent Gatto and Sebastian Gibb

    -

    Examples

    
@@ -114,22 +99,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/getVariableName.html b/reference/getVariableName.html index 5c8093ee..2a657a22 100644 --- a/reference/getVariableName.html +++ b/reference/getVariableName.html @@ -3,8 +3,6 @@ - -
    - - -
    @@ -69,29 +61,21 @@

    Return a variable name

    Source: R/utils.R
    -

    Return the name of variable varname in call match_call.

    - 
    getVariableName(match_call, varname)
    -

    Arguments

    match_call

    An object of class call, as returned by match.call.

    - -
    varname

    An character of length 1 which is looked up in match_call.

    -

    Value

    - -

    A character with the name of the variable passed as parameter varname in parent close of match_call.

    @@ -99,7 +83,6 @@

    Value

    Author

    Laurent Gatto

    -

    Examples

    a <- 1
@@ -116,22 +99,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/grepEcols.html b/reference/grepEcols.html index c29d4929..ed42d387 100644 --- a/reference/grepEcols.html +++ b/reference/grepEcols.html @@ -6,8 +6,6 @@ - -
    - - -
    @@ -72,47 +64,35 @@

    Returns the matching column names of indices.

    Source: R/utils.R
    -

    Given a text spread sheet f and a pattern to be matched to its header (first line in the file), the function returns the matching columns names or indices of the corresponding data.frame.

    - 
    grepEcols(f, pattern, ..., n = 1)
 
 getEcols(f, ..., n = 1)
    -

    Arguments

    f

    A connection object or a character string to be read in with readLines(f, n = 1).

    - -
    pattern

    A character string containing a regular expression to be matched to the file's header.

    - -
    ...

    Additional parameters passed to strsplit to split the file header into individual column names.

    - -
    n

    An integer specifying which line in file f to grep (get). Default is 1. Note that this argument must be named.

    -

    Value

    - -

    Depending on value, the matching column names of indices. In case of getEcols, a character of column names.

    @@ -138,28 +118,17 @@

    See also

    Author

    Laurent Gatto

    -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/hasSpectraOrChromatograms.html b/reference/hasSpectraOrChromatograms.html index b18826b7..218d29e7 100644 --- a/reference/hasSpectraOrChromatograms.html +++ b/reference/hasSpectraOrChromatograms.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,28 +62,22 @@

    Checks if raw data files have any spectra or chromatograms

    Source: R/utils.R
    -

    Helper functions to check whether raw files contain spectra or chromatograms.

    - 
    hasSpectra(files)
 
 hasChromatograms(files)
    -

    Arguments

    files

    A character() with raw data filenames.

    -

    Value

    - -

    A logical(n) where n == length(x) with TRUE if that files contains at least one spectrum, FALSE otherwise.

    @@ -99,7 +85,6 @@

    Value

    Author

    Laurent Gatto

    -

    Examples

    f <- msdata::proteomics(full.names = TRUE)[1:2]
@@ -120,22 +105,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/iPQF.html b/reference/iPQF.html index 00a31bac..1487ec13 100644 --- a/reference/iPQF.html +++ b/reference/iPQF.html @@ -11,8 +11,6 @@ - -
    - - -
    @@ -77,7 +69,6 @@

    iPQF: iTRAQ (and TMT) Protein Quantification based on Features

    Source: R/iPQF.R
    -

    The iPQF spectra-to-protein summarisation method integrates peptide spectra characteristics and quantitative values for protein @@ -89,7 +80,6 @@

    iPQF: iTRAQ (and TMT) Protein Quantification based on Features

    See also combineFeatures for a more general overview of feature aggregation and examples.

    - 
    iPQF(
   object,
@@ -100,50 +90,36 @@ 
    iPQF: iTRAQ (and TMT) Protein Quantification based on Features
    
   feature.weight = c(7, 6, 4, 3, 2, 1, 5)^2
 )
    -

    Arguments

    object

    An instance of class MSnSet containing absolute ion intensities.

    - -
    groupBy

    Vector defining spectra to protein matching. Generally, this is a feature variable such as fData(object)$accession.

    - -
    low.support.filter

    A logical specifying if proteins being supported by only 1-2 peptide spectra should be filtered out. Default is FALSE.

    - -
    ratio.calc

    Either "none" (don't calculate any ratios), "sum" (default), or a specific channel (one of sampleNames(object)) defining how to calculate relative peptides intensities.

    - -
    method.combine

    A logical defining whether to further use median polish to combine features.

    - -
    feature.weight

    Vector "numeric" giving weight to the different features. Default is the squared order of the features redundant -unique-distance metric, charge state, ion intensity, sequence length, identification score, modification state, and mass based on a robustness analysis.

    -

    Value

    - -

    A matrix with estimated protein ratios.

    @@ -158,7 +134,6 @@

    References

    Author

    Martina Fischer

    -

    Examples

    data(msnset2)
@@ -192,22 +167,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/iTRAQ4.html b/reference/iTRAQ4.html index d24391c4..1be6767d 100644 --- a/reference/iTRAQ4.html +++ b/reference/iTRAQ4.html @@ -9,8 +9,6 @@ - -
    - - -

    iTRAQ 4-plex set

    -
    -

    This instance of class "ReporterIons" corresponds to the iTRAQ 4-plex set, i.e the 114, 115, 116 and 117 isobaric @@ -85,14 +75,12 @@

    iTRAQ 4-plex set

    MSMS spectra (see "Spectrum2") as well as for quantification (see quantify).

    - 
    iTRAQ4
 iTRAQ5
 iTRAQ8
 iTRAQ9
    -

    References

    Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, @@ -107,7 +95,6 @@

    References

    See also

    TMT6.

    -

    Examples

    iTRAQ4
@@ -142,22 +129,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/imageNA2.html b/reference/imageNA2.html index da5f504f..1bd72a44 100644 --- a/reference/imageNA2.html +++ b/reference/imageNA2.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,12 +62,10 @@

    NA heatmap visualisation for 2 groups

    Source: R/missing-data.R
    -

    Produces a heatmap after reordring rows and columsn to highlight missing value patterns.

    - 
    imageNA2(
   object,
@@ -87,52 +77,36 @@ 
    NA heatmap visualisation for 2 groups
    
   ...
 )
    -

    Arguments

    object

    An instance of class MSnSet

    - -
    pcol

    Either the name of a phenoData variable to be used to determine the group structure or a factor or any object that can be coerced as a factor of length equal to nrow(object). The resulting factor must have 2 levels. If missing (default) image(object) is called.

    - -
    Rowv

    Determines if and how the rows/features are reordered. If missing (default), rows are reordered according to order((nNA1 + 1)^2/(nNA2 + 1)), where NA1 and NA2 are the number of missing values in each group. Use a vector of numerics of feautre names to customise row order.

    - -
    Colv

    A logical that determines if columns/samples are reordered. Default is TRUE.

    - -
    useGroupMean

    Replace individual feature intensities by the group mean intensity. Default is FALSE.

    - -
    plot

    A logical specifying of an image should be produced. Default is TRUE.

    - -
    ...

    Additional arguments passed to image.

    -

    Value

    - -

    Used for its side effect of plotting. Invisibly returns Rovw and Colv.

    @@ -140,7 +114,6 @@

    Value

    Author

    Laurent Gatto, Samuel Wieczorek and Thomas Burger

    -

    Examples

    library("pRolocdata")
@@ -165,22 +138,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/impute.html b/reference/impute.html index 0af75a84..99af3558 100644 --- a/reference/impute.html +++ b/reference/impute.html @@ -10,8 +10,6 @@ - -
    - - -
    @@ -76,7 +68,6 @@

    Quantitative proteomics data imputation

    Source: R/imputation.R
    -

    The impute method performs data imputation on MSnSet instances using a variety of methods.

    @@ -87,31 +78,23 @@

    Quantitative proteomics data imputation

    See MsCoreUtils::impute_matrix() for details on the different imputation methods available and strategies.

    - 
    # S4 method for class 'MSnSet'
 impute(object, method, ...)
    -

    Arguments

    object

    An MSnSet object with missing values to be imputed.

    - -
    method

    character(1) defining the imputation method. See MsCoreUtils::imputeMethods() for available ones. See MsCoreUtils::impute_matrix() for details.

    - -
    ...

    Additional parameters passed to the inner imputation function. See MsCoreUtils::impute_matrix() for details.

    -
    -

    Examples

    
@@ -151,7 +134,7 @@ 
    Examples
    
 #> experimentData: use 'experimentData(object)'
 #> Annotation:  
 #> - - - Processing information - - -
-#> Data imputation using min Wed May  1 08:22:54 2024 
+#> Data imputation using min Wed May 15 16:30:20 2024 
 #>  MSnbase version: 1.15.6 
 
 if (require("imputeLCMD")) {
@@ -198,7 +181,7 @@ 
    Examples
    
 #> experimentData: use 'experimentData(object)'
 #> Annotation:  
 #> - - - Processing information - - -
-#> Data imputation using MinDet Wed May  1 08:22:54 2024 
+#> Data imputation using MinDet Wed May 15 16:30:20 2024 
 #>  MSnbase version: 1.15.6 
 
 if (require("norm"))
@@ -222,7 +205,7 @@ 
    Examples
    
 #> experimentData: use 'experimentData(object)'
 #> Annotation:  
 #> - - - Processing information - - -
-#> Data imputation using MLE Wed May  1 08:22:54 2024 
+#> Data imputation using MLE Wed May 15 16:30:21 2024 
 #>  MSnbase version: 1.15.6 
 
 impute(naset, "mixed",
@@ -245,7 +228,7 @@ 
    Examples
    
 #> experimentData: use 'experimentData(object)'
 #> Annotation:  
 #> - - - Processing information - - -
-#> Data imputation using mixed Wed May  1 08:22:54 2024 
+#> Data imputation using mixed Wed May 15 16:30:21 2024 
 #>  MSnbase version: 1.15.6 
 
 
@@ -278,22 +261,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/index.html b/reference/index.html index 66ef8341..1ba22e77 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,10 +1,8 @@ -Function reference • MSnbasePackage index • MSnbase - -
    - - -

    Reference

    -

    All functions

    @@ -457,27 +448,16 @@

    All functions

    Export an MzTab object as mzTab file.
    -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/isCentroidedFromFile.html b/reference/isCentroidedFromFile.html index 965c7a97..197edc68 100644 --- a/reference/isCentroidedFromFile.html +++ b/reference/isCentroidedFromFile.html @@ -6,8 +6,6 @@ - -
    - - -
    @@ -72,28 +64,22 @@

    Get mode from mzML data file

    Source: R/functions-OnDiskMSnExp.R
    -

    The function extracts the mode (profile or centroided) from the raw mass spectrometry file by parsing the mzML file directly. If the object x stems from any other type of file, NAs are returned.

    - 
    isCentroidedFromFile(x)
    -

    Arguments

    x

    An object of class OnDiskMSnExp.

    -

    Value

    - -

    A named logical vector of the same length as x.

    @@ -107,7 +93,6 @@

    Details

    Author

    Laurent Gatto

    -

    Examples

    library("msdata")
@@ -126,22 +111,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/itraqdata.html b/reference/itraqdata.html index 2bd16302..a4799e07 100644 --- a/reference/itraqdata.html +++ b/reference/itraqdata.html @@ -1,6 +1,5 @@ Example MSnExp and MSnSet data sets — itraqdata • MSnbase -#> Set 150 values to NA Wed May 1 08:22:57 2024 +#> Set 150 values to NA Wed May 15 16:30:24 2024 #> MSnbase version: 1.17.12 sum(is.na(dunkleyNA)) #> [1] 150 @@ -180,7 +151,7 @@

    Examples

    dunkleyNA <- makeNaData(dunkley2006, nNA = 150, exclude = 1:10) processingData(dunkleyNA) #> - - - Processing information - - - -#> Set 150 values to NA Wed May 1 08:22:57 2024 +#> Set 150 values to NA Wed May 15 16:30:24 2024 #> (excluding 10 features) #> MSnbase version: 1.17.12 table(fData(dunkleyNA)$nNA[1:10]) @@ -202,9 +173,9 @@

    Examples

    #> Loaded on Thu Jul 16 22:53:08 2015. #> Normalised to sum of intensities. #> Added markers from 'mrk' marker vector. Thu Jul 16 22:53:08 2015 -#> Subset [689,16][100,5] Wed May 1 08:22:58 2024 +#> Subset [689,16][100,5] Wed May 15 16:30:24 2024 #> Set (1,2,3,4,5) NAs in (10,10,10,10,10) rows, -#> respectively Wed May 1 08:22:58 2024 +#> respectively Wed May 15 16:30:24 2024 #> MSnbase version: 1.17.12 (res <- table(fData(x)$nNA)) #> @@ -223,9 +194,9 @@

    Examples

    #> Loaded on Thu Jul 16 22:53:08 2015. #> Normalised to sum of intensities. #> Added markers from 'mrk' marker vector. Thu Jul 16 22:53:08 2015 -#> Subset [689,16][100,10] Wed May 1 08:22:58 2024 +#> Subset [689,16][100,10] Wed May 15 16:30:24 2024 #> Set (3,8,1,4) NAs in (5,12,11,8) rows, -#> respectively Wed May 1 08:22:58 2024 +#> respectively Wed May 15 16:30:24 2024 #> MSnbase version: 1.17.12 (res2 <- table(fData(x2)$nNA)) #> @@ -244,9 +215,9 @@

    Examples

    #> Loaded on Thu Jul 16 22:53:08 2015. #> Normalised to sum of intensities. #> Added markers from 'mrk' marker vector. Thu Jul 16 22:53:08 2015 -#> Subset [689,16][100,10] Wed May 1 08:22:58 2024 +#> Subset [689,16][100,10] Wed May 15 16:30:24 2024 #> Set (3,8,1,3) NAs in (5,12,11,8) rows, -#> respectively Wed May 1 08:22:58 2024 +#> respectively Wed May 15 16:30:24 2024 #> MSnbase version: 1.17.12 (res3 <- table(fData(x3)$nNA)) #> @@ -259,22 +230,12 @@

    Examples

    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/meanMzInts.html b/reference/meanMzInts.html index 69e83753..16b1f50d 100644 --- a/reference/meanMzInts.html +++ b/reference/meanMzInts.html @@ -9,8 +9,6 @@ - -
    - - -
    @@ -75,7 +67,6 @@

    Combine a list of spectra to a single spectrum

    Source: R/functions-Spectrum.R
    -

    Combine peaks from several spectra into a single spectrum. Intensity and m/z values from the input spectra are aggregated into a single peak if @@ -85,7 +76,6 @@

    Combine a list of spectra to a single spectrum

    values of grouped mass peaks are aggregated with the intensityFun, m/z values by the mean, or intensity weighted mean if weighted = TRUE.

    - 
    meanMzInts(
   x,
@@ -99,48 +89,33 @@ 
    Combine a list of spectra to a single spectrum
    
   unionPeaks = TRUE
 )
    -

    Arguments

    x

    list of Spectrum objects.

    - -
    ...

    additional parameters that are passed to intensityFun.

    - -
    intensityFun

    function to aggregate the intensity values per m/z group. Should be a function or the name of a function. The function is expected to return a numeric(1).

    - -
    weighted

    logical(1) whether m/z values per m/z group should be aggregated with an intensity-weighted mean. The default is to report the mean m/z.

    - -
    main

    integer(1) defining the main spectrum, i.e. the spectrum which m/z and intensity values get replaced and is returned. By default the first spectrum in x is used.

    - -
    mzd

    numeric(1) defining the maximal m/z difference below which mass peaks are considered to represent the same ion/mass peak. Intensity values for such grouped mass peaks are aggregated. If not specified this value is estimated from the distribution of differences of m/z values from the provided spectra (see details).

    - -
    ppm

    numeric(1) allowing to perform a m/z dependent grouping of mass peaks. See details for more information.

    - -
    timeDomain

    logical(1) whether definition of the m/z values to be combined into one m/z is performed on m/z values @@ -149,19 +124,14 @@

    Arguments

    on the time domain (see details). Note that a pre-defined mzd should also be estimated on the square root of m/z values if timeDomain = TRUE.

    - -
    unionPeaks

    logical(1) whether the union of all peaks (peak groups) from all spectra are reported or only peak groups that contain peaks that are present in the main spectrum (defined by main). The default is to report the union of peaks from all spectra.

    -

    Value

    - -

    Spectrum with m/z and intensity values representing the aggregated values across the provided spectra. The returned spectrum contains the union of all peaks from all spectra (if unionPeaks = TRUE), or the same number of @@ -212,14 +182,13 @@

    See also

    a spectrum.

    combineSpectraMovingWindow() for the function to combine consecutive spectra of an MSnExp object using a moving window approach.

    -

    Other spectra combination functions: +

    Other spectra combination functions: consensusSpectrum()

    Author

    Johannes Rainer, Sigurdur Smarason

    -

    Examples

    
@@ -261,22 +230,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/missing-data.html b/reference/missing-data.html index c89d6b68..a41c3be6 100644 --- a/reference/missing-data.html +++ b/reference/missing-data.html @@ -1,6 +1,5 @@ Documenting missing data visualisation — missing-data • MSnbase - -
    - - -

    Documenting missing data visualisation

    -
    -
    - -

    There is a need for adequate handling of missing value impuation in quantitative proteomics. Before developing a framework to handle missing data imputation optimally, we propose a set of visualisation @@ -87,8 +74,6 @@

    Documenting missing data visualisation

    progress and ideas that will eventually materialise in exported functionality in the MSnbase package.

    - -

    Details

    The explore the structure of missing values, we propose to

    @@ -112,7 +97,6 @@

    Author

    Laurent Gatto <lg390@cam.ac.uk>, Samuel Wieczorek and Thomas Burger

    -

    Examples

    ## Other suggestions
@@ -170,22 +154,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/mzRident2dfr.html b/reference/mzRident2dfr.html index be70bd41..de57abd7 100644 --- a/reference/mzRident2dfr.html +++ b/reference/mzRident2dfr.html @@ -10,8 +10,6 @@ - -
    - - -
    @@ -76,7 +68,6 @@

    Coerce identification data to a data.frame

    Source: R/functions-mzR.R
    -

    A function to convert the identification data contained in an mzRident object to a data.frame. Each row represents @@ -87,22 +78,15 @@

    Coerce identification data to a data.frame

    information pertaining a scan, use reduce.

    - -

    Arguments

    from

    An object of class mzRident defined in the mzR package.

    -

    Value

    - -

    A data.frame

    - -

    Details

    @@ -113,7 +97,6 @@

    Details

    Author

    Laurent Gatto

    -

    Examples

    ## find path to a mzIdentML file
@@ -168,22 +151,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/nFeatures.html b/reference/nFeatures.html index 3cab9d8a..ef5521c7 100644 --- a/reference/nFeatures.html +++ b/reference/nFeatures.html @@ -5,8 +5,6 @@ - -
    - - -
    @@ -71,32 +63,24 @@

    How many features in a group?

    Source: R/functions-MSnSet.R
    -

    This function computes the number of features in the group defined by the feature variable fcol and appends this information in the feature data of object.

    - 
    nFeatures(object, fcol)
    -

    Arguments

    object

    An instance of class MSnSet.

    - -
    fcol

    Feature variable defining the feature grouping structure.

    -

    Value

    - -

    An updated MSnSet with a new feature variable fcol.nFeatures.

    @@ -104,7 +88,6 @@

    Value

    Author

    Laurent Gatto

    -

    Examples

    library(pRolocdata)
@@ -131,22 +114,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/nQuants.html b/reference/nQuants.html index 93a06528..29fbf803 100644 --- a/reference/nQuants.html +++ b/reference/nQuants.html @@ -7,8 +7,6 @@ - -
    - - -
    @@ -73,7 +65,6 @@

    Count the number of quantitfied features.

    Source: R/functions-MSnSet.R
    -

    This function counts the number of quantified features, i.e non NA quantitation values, for each group of features @@ -81,34 +72,24 @@

    Count the number of quantitfied features.

    The group of features are defined by a feature variable names, i.e the name of a column of fData(object).

    - 
    nQuants(x, groupBy)
    -

    Arguments

    x

    An instance of class "MSnSet".

    - -
    groupBy

    An object of class factor defining how to summerise the features. (Note that this parameter was previously named fcol and referred to a feature variable label. This has been updated in version 1.19.12 for consistency with other functions.)

    -

    Value

    - -

    A matrix of dimensions length(levels(groupBy)) by ncol(x)

    - - -

    A matrix of dimensions length(levels(factor(fData(object)[, fcol]))) by ncol(object) of integers.

    @@ -129,7 +110,6 @@

    Author

    Laurent Gatto lg390@cam.ac.uk, Sebastian Gibb mail@sebastiangibb.de

    -

    Examples

    data(msnset)
@@ -163,22 +143,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/naplot.html b/reference/naplot.html index b5f9c70a..da3aa8e2 100644 --- a/reference/naplot.html +++ b/reference/naplot.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,12 +62,10 @@

    Overview of missing value

    Source: R/missing-data.R
    -

    Visualise missing values as a heatmap and barplots along the samples and features.

    - 
    naplot(
   object,
@@ -85,45 +75,30 @@ 
    Overview of missing value
    
   ...
 )
    -

    Arguments

    object

    An object of class MSnSet.

    - -
    verbose

    If verbose (default is isMSnbaseVerbose()), print a table of missing values.

    - -
    reorderRows

    If reorderRows (default is TRUE) rows are ordered by number of NA.

    - -
    reorderColumns

    If reorderColumns (default is TRUE) columns are ordered by number of NA.

    - -
    ...

    Additional parameters passed to image2.

    -

    Value

    - -

    Used for its side effect. Invisibly returns NULL

    - -

    Author

    Laurent Gatto

    -

    Examples

    data(naset)
@@ -136,22 +111,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/navMS.html b/reference/navMS.html index 9d12a045..4d022465 100644 --- a/reference/navMS.html +++ b/reference/navMS.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,12 +62,10 @@

    Navigate an MSnExp object

    Source: R/nav.R
    -

    Navigate an MSnExp object by moving to the next or previous spectrum.

    - 
    navMS(i, object, msLevel, nav = c("nextMS", "prevMS"), ...)
 
@@ -83,36 +73,24 @@ 
    Navigate an MSnExp object
    
 
 prevMS(...)
    -

    Arguments

    i

    The name or index of the current spectrum

    - -
    object

    The MSnExp object

    - -
    msLevel

    The MS level of the next or previous spectrum. If missing (default), then the level of the current spectrum is used.

    - -
    nav

    One of "nextMS" or "prevMS", to obtain the next or previous spectrum of level msLevel.

    - -
    ...

    Additional parameters. Currently ignored.

    -

    Value

    - -

    An object of class Spectrum1 or Spectrum2, depending on the value of msLevel or NULL, of no spectrum is found.

    @@ -121,7 +99,6 @@

    Value

    Author

    Laurent Gatto

    -

    Examples

    f <- msdata::proteomics(full.names = TRUE, pattern = "MS3")
@@ -177,22 +154,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/normToReference.html b/reference/normToReference.html index 9018eaf4..3d868248 100644 --- a/reference/normToReference.html +++ b/reference/normToReference.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,12 +62,10 @@

    Combine peptides into proteins.

    Source: R/NTR.R
    -

    This function combines peptides into their proteins by normalising the intensity values to a reference run/sample for each protein.

    - 
    normToReference(
   x,
@@ -83,28 +73,20 @@ 
    Combine peptides into proteins.
    
   reference = .referenceFractionValues(x = x, group = group)
 )
    -

    Arguments

    x

    matrix, exprs matrix of an MSnSet object.

    - -
    group

    double or factor, grouping variable, i.e. protein accession; has to be of length equal nrow(x).

    - -
    reference

    double, vector of reference values, has to be of the same length as group and nrow(x).

    -

    Value

    - -

    a matrix with one row per protein.

    @@ -142,7 +124,6 @@

    See also

    Author

    Sebastian Gibb mail@sebastiangibb.de, Pavel Shliaha

    -

    Examples

    library("MSnbase")
@@ -170,8 +151,8 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> iTRAQ4 quantification by trapezoidation: Wed Apr  1 21:41:53 2015 
-#> Combined 55 features into 40 using mean: Wed May  1 08:23:05 2024 
-#>  MSnbase version: 2.31.0 
+#> Combined 55 features into 40 using mean: Wed May 15 16:30:32 2024 
+#>  MSnbase version: 2.31.1 
 
 # use a user-given reference
 combineFeatures(msnset, groupBy=fData(msnset)$ProteinAccession,
@@ -196,8 +177,8 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> iTRAQ4 quantification by trapezoidation: Wed Apr  1 21:41:53 2015 
-#> Combined 55 features into 40 using mean: Wed May  1 08:23:05 2024 
-#>  MSnbase version: 2.31.0 
+#> Combined 55 features into 40 using mean: Wed May 15 16:30:32 2024 
+#>  MSnbase version: 2.31.1
    @@ -206,22 +187,12 @@

    Examples

    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/normalise-methods.html b/reference/normalise-methods.html index af4b07c4..4fb08553 100644 --- a/reference/normalise-methods.html +++ b/reference/normalise-methods.html @@ -1,14 +1,14 @@ Normalisation of MSnExp, MSnSet and Spectrum objects — normalise-methods • MSnbase - -
    - - -

    Normalisation of MSnExp, MSnSet and Spectrum objects

    -
    -

    The normalise method (also available as normalize) - performs basic normalisation on spectra - intensities of single spectra ("Spectrum" or + performs basic normalisation on spectra + intensities of single spectra ("Spectrum" or "Spectrum2" objects), whole experiments ("MSnExp" objects) or quantified expression data ("MSnSet" objects).

    Raw spectra and experiments are normalised using max or - sum only. For MSMS spectra could be normalised to their + sum only. For MSMS spectra could be normalised to their precursor additionally. Each peak intensity is divided by the - highest intensity in the spectrum, the sum of intensities or the intensity + highest intensity in the spectrum, the sum of intensities or the intensity of the precursor. These methods aim at facilitating relative peaks heights between different spectra.

    @@ -121,7 +111,7 @@

    Normalisation of MSnExp, MSnSet and Spectrum center.median, .median, quantiles.robust or vsn. For sum and max, each feature's reporter intensity is divided by the maximum or the sum respectively. These two - methods are applied along the features (rows).

    + methods are applied along the features (rows).

    center.mean and center.median translate the respective sample (column) intensities according to the column mean or median. diff.median translates all samples (columns) so that @@ -132,57 +122,44 @@

    Normalisation of MSnExp, MSnSet and Spectrum package. vsn uses the vsn2 function from the vsn package. Note that the latter also glog-transforms the intensities. See respective manuals for more details and function - arguments.

    + arguments.

    A scale method, mimicking the base scale method exists for "MSnSet" instances. See ?base::scale for details.

    - -

    Arguments

    object
    -

    An object of class "Spectrum", +

    An object of class "Spectrum", "Spectrum2", "MSnExp" or "MSnSet".

    -
    method

    A character vector of length one that describes how to normalise the object. See description for details.

    -
    ...

    Additional arguments passed to the normalisation function.

    -

    Methods

    The normalise methods:

    signature(object = "MSnSet", method = "character")

    Normalises the object reporter ions intensities using method.

    -
    signature(object = "MSnExp", method = "character")

    Normalises the object peak intensities using method.

    -
    signature(object = "Spectrum", method = "character")

    Normalises the object peak intensities using method.

    -
    signature(object = "Spectrum2", method = "character", precursorIntensity)

    Normalises the object peak intensities using - method. If method == "precursor", + method. If method == "precursor", precursorIntensity allows to specify the intensity of the precursor manually.

    - -

    The scale method:

    signature(x = "MSnSet", center = "logical", scale = "logical")

    See ?base::scale.

    - -
    -

    Examples

    ## quantifying full experiment
@@ -206,7 +183,7 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> iTRAQ4 quantification by trapezoidation: Wed Apr  1 21:41:53 2015 
-#> Normalised (quantiles): Wed May  1 08:23:05 2024 
+#> Normalised (quantiles): Wed May 15 16:30:32 2024 
 #>  MSnbase version: 1.1.22
    @@ -215,22 +192,12 @@

    Examples

    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/npcv.html b/reference/npcv.html index 1354f55c..b9a71855 100644 --- a/reference/npcv.html +++ b/reference/npcv.html @@ -6,8 +6,6 @@ - -
    - - -
    @@ -72,34 +64,26 @@

    Non-parametric coefficient of variation

    Source: R/utils.R
    -

    Calculates a non-parametric version of the coefficient of variation where the standard deviation is replaced by the median absolute deviations (see mad for details) and divided by the absolute value of the mean.

    - 
    npcv(x, na.rm = TRUE)
    -

    Arguments

    x

    A numeric.

    - -
    na.rm

    A logical (default is TRUE indicating whether NA values should be stripped before the computation of the median absolute deviation and mean.

    -

    Value

    - -

    A numeric.

    @@ -111,7 +95,6 @@

    Details

    Author

    Laurent Gatto

    -

    Examples

    set.seed(1)
@@ -133,22 +116,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/pSet-class.html b/reference/pSet-class.html index c19253ae..2c8172bc 100644 --- a/reference/pSet-class.html +++ b/reference/pSet-class.html @@ -7,8 +7,6 @@ - -
    - - -

    Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

    -
    -

    Container for high-throughput mass-spectrometry assays and experimental metadata. This class is based on Biobase's @@ -81,8 +71,6 @@

    Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

    that 'assayData' slot is an environment contain objects of class "Spectrum".

    - -

    Objects from the Class

    A virtual Class: No objects may be created from it. @@ -94,14 +82,12 @@

    Slots

    Object of class "environment" containing the MS spectra (see "Spectrum1" and "Spectrum2").

    -
    phenoData:

    Object of class "AnnotatedDataFrame" containing experimenter-supplied variables describing sample (i.e the individual tags for an labelled MS experiment) See phenoData for more details.

    -
    featureData:

    Object of class "AnnotatedDataFrame" containing variables @@ -109,32 +95,25 @@

    Slots

    peptide sequence, identification score,... (inherited from "eSet"). See featureData for more details.

    -
    experimentData:

    Object of class "MIAPE", containing details of experimental methods. See experimentData for more details.

    -
    protocolData:

    Object of class "AnnotatedDataFrame" containing equipment-generated variables (inherited from "eSet"). See protocolData for more details.

    -
    processingData:

    Object of class "MSnProcess" that records all processing.

    -
    .cache:

    Object of class environment used to cache data. Under development.

    -
    .__classVersion__:

    Object of class "Versions" describing the versions of the class.

    - -

    Extends

    @@ -148,219 +127,168 @@

    Methods

    [

    signature(x = "pSet"): Subset current object and return object of same class.

    -
    [[

    signature(x = "pSet"): Direct access to individual spectra.

    -
    $

    signature(x = "pSet"): directly access a specific sample annotation column from the pData.

    -
    $<-

    signature(x = "pSet"): replace or add a sample annotation column in the pData.

    -
    abstract

    Access abstract in experimentData.

    -
    assayData

    signature(object = "pSet"): Access the assayData slot. Returns an environment.

    -
    desciption

    signature(x = "pSet"): Synonymous with experimentData.

    -
    dim

    signature(x = "pSet"): Returns the dimensions of the phenoData slot.

    -
    experimentData

    signature(x = "pSet"): Access details of experimental methods.

    -
    featureData

    signature(x = "pSet"): Access the featureData slot.

    -
    fData

    signature(x = "pSet"): Access feature data information.

    -
    featureNames

    signature(x = "pSet"): Coordinate access of feature names (e.g spectra, peptides or proteins) in assayData slot.

    -
    fileNames

    signature(object = "pSet"): Access file names in the processingData slot.

    -
    fromFile

    signature(object = "pSet"): Access raw data file indexes (to be found in the processingData slot) from which the individual object's spectra where read from.

    -
    centroided

    signature(object = "pSet"): Indicates whether individual spectra are centroided ('TRUE') of uncentroided ('FALSE'). Use centroided(object) <- value to update a whole experiment, ensuring that object and value have the same length.

    -
    smoothed

    signature(object = "pSet"): Indicates whether individual spectra are smoothed ('TRUE') of unsmoothed ('FALSE'). Use smoothed(object) <- value to update a whole experiment, ensuring that object and value have the same length.

    -
    fvarMetadata

    signature(x = "pSet"): Access metadata describing features reported in fData.

    -
    fvarLabels

    signature(x = "pSet"): Access variable labels in featureData.

    -
    length

    signature(x = "pSet"): Returns the number of features in the assayData slot.

    -
    notes

    signature(x = "pSet"): Retrieve and unstructured notes associated with pSet in the experimentData slot.

    -
    pData

    signature(x = "pSet"): Access sample data information.

    -
    pData<-

    signature(x = "pSet", value): Replace sample data information with value, value being a data.frame.

    -
    phenoData

    signature(x = "pSet"): Access the phenoData slot.

    -
    phenoData<-

    signature(x = "pSet", value): Replace sample data information with value. value can be a data.frame or an AnnotatedDataFrame.

    -
    processingData

    signature(object = "pSet"): Access the processingData slot.

    -
    protocolData

    signature(x = "pSet"): Access the protocolData slot.

    -
    pubMedIds

    signature(x = "pSet"): Access PMIDs in experimentData.

    -
    sampleNames

    signature(x = "pSet"): Access sample names in phenoData. A replacement method is also available.

    -
    spectra

    signature(x = "pSet", ...): Access the assayData slot, returning the features as a list. Additional arguments are currently ignored.

    -
    varMetadata

    signature(x = "pSet"): Access metadata describing variables reported in pData.

    -
    varLabels

    signature(x = "pSet"): Access variable labels in phenoData.

    -
    acquisitionNum

    signature(object = "pSet"): Accessor for spectra acquisition numbers.

    -
    scanIndex

    signature(object = "pSet"): Accessor for spectra scan indices.

    -
    collisionEnergy

    signature(object = "pSet"): Accessor for MS2 spectra collision energies.

    -
    intensity

    signature(object = "pSet", ...): Accessor for spectra instenities, returned as named list. Additional arguments are currently ignored.

    -
    msInfo

    signature(object = "pSet"): Prints the MIAPE-MS meta-data stored in the experimentData slot.

    -
    msLevel

    signature(object = "pSet"): Accessor for spectra MS levels.

    -
    mz

    signature(object = "pSet", ...): Accessor for spectra M/Z values, returned as a named list. Additional arguments are currently ignored.

    -
    peaksCount

    signature(object = "pSet"): Accessor for spectra preak counts.

    -
    peaksCount

    signature(object = "pSet", scans = "numeric"): Accessor to scans spectra preak counts.

    -
    polarity

    signature(object = "pSet"): Accessor for MS1 spectra polarities.

    -
    precursorCharge

    signature(object = "pSet"): Accessor for MS2 precursor charges.

    -
    precursorIntensity

    signature(object = "pSet"): Accessor for MS2 precursor intensity.

    -
    precursorMz

    signature(object = "pSet"): Accessor for MS2 precursor M/Z values.

    -
    precAcquisitionNum

    signature(object = "pSet"): Accessor for MS2 precursor scan numbers.

    -
    precScanNum

    see precAcquisitionNum.

    -
    rtime

    signature(object = "pSet", ...): Accessor for spectra retention times. Additional arguments are currently ignored.

    -
    tic

    signature(object = "pSet", ...): Accessor for spectra total ion counts. Additional arguments are currently ignored.

    -
    ionCount

    signature(object = "pSet"): Accessor for spectra total ion current.

    -
    header

    signature(object = "pSet"): Returns a data frame containing all available spectra parameters (MSn only).

    -
    header

    signature(object = "pSet", scans = "numeric"): Returns a data frame containing scans spectra parameters (MSn only).

    -
    spectrapply

    spectrapply(signature(object = "pSet"), FUN = NULL, BPPARAM = bpparam(), ...): applies the function FUN to each @@ -370,23 +298,16 @@

    Methods

    BPPARAM allows to specify how and if parallel processing should be enabled.

    Returns a list with the result for each of spectrum.

    - -
    isolationWindowLowerMz

    isolationWindowLowerMz(object = "pSet"): return the lower m/z boundary for the isolation window. Note that this method is at present only available for OnDiskMSnExp objects.

    - -
    isolationWindowUpperMz

    isolationWindowUpperMz(object = "pSet"): return the upper m/z boundary for the isolation window. Note that this method is at present only available for OnDiskMSnExp objects.

    - - -

    Additional accessors for the experimental metadata (experimentData slot) are defined. See "MIAPE" for details.

    @@ -404,7 +325,6 @@

    See also

    "MSnExp" for an instantiatable application of pSet.

    -

    Examples

    showClass("pSet")
@@ -433,22 +353,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/pickPeaks-method.html b/reference/pickPeaks-method.html index 455b4aa0..701c8570 100644 --- a/reference/pickPeaks-method.html +++ b/reference/pickPeaks-method.html @@ -10,7 +10,7 @@ The method supports also to optionally refine the m/z value of the identified centroids by considering data points that belong (most likely) to the same mass peak. The m/z value is calculated as an - intensity weighted average of the m/z values within the peak region. + intensity weighted average of the m/z values within the peak region. How the peak region is defined depends on the method chosen: refineMz = "kNeighbors": m/z values (and their respective intensities) of the2 * k closest signals to the centroid are @@ -24,14 +24,12 @@ default the descend is stopped when the first signal that is equal or larger than the last observed one is encountered. Setting stopAtTwo = TRUE, two consecutively increasing signals are - required. + required. By default (refineMz = "none", simply the m/z of the largest signal (the identified centroid) is reported. See below for examples."> - -
    - - -

    Peak Detection for 'MSnExp' or 'Spectrum' instances

    -
    -

    This method performs a peak picking on individual spectra (Spectrum instances) or whole experiments (MSnExp instances) to @@ -109,7 +99,7 @@

    Peak Detection for 'MSnExp' or 'Spectrum' instances

    The method supports also to optionally refine the m/z value of the identified centroids by considering data points that belong (most likely) to the same mass peak. The m/z value is calculated as an - intensity weighted average of the m/z values within the peak region. + intensity weighted average of the m/z values within the peak region. How the peak region is defined depends on the method chosen:

    refineMz = "kNeighbors": m/z values (and their respective intensities) of the2 * k closest signals to the centroid are @@ -123,12 +113,10 @@

    Peak Detection for 'MSnExp' or 'Spectrum' instances

    default the descend is stopped when the first signal that is equal or larger than the last observed one is encountered. Setting stopAtTwo = TRUE, two consecutively increasing signals are - required.

    + required.

    By default (refineMz = "none", simply the m/z of the largest signal (the identified centroid) is reported. See below for examples.

    - -

    Methods

    signature(x = "MSnExp", halfWindowSize = "integer", @@ -154,18 +142,15 @@

    Methods

    details. refineMethod = "kNeighbors" supports additional argument k and refineMethod = "descendPeak" arguments signalPercentage and stopAtTwo. See - description above for more details.

    + description above for more details.

    This method displays a progress bar if verbose = TRUE. Returns an MSnExp instance with centroided spectra.

    -
    signature(x = "Spectrum", method = "character", halfWindowSize = "integer", ...)

    Performs the peak picking for the spectrum (Spectrum instance). This method is the same as above but returns a centroided Spectrum instead of an MSnExp object. It has no verbose argument. Please read the details for the above MSnExp method.

    - -

    Author

    @@ -185,7 +170,6 @@

    References

    Bioinformatics 28: 2270-2271. http://strimmerlab.org/software/maldiquant/

    -

    Examples

    sp1 <- new("Spectrum1",
@@ -202,11 +186,11 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> Updated from version 0.3.0 to 0.3.1 [Fri Jul  8 20:23:25 2016] 
-#> peak picking: MAD noise estimation and none centroid m/z refinement on spectra of MS level(s)2 [Wed May  1 08:23:06 2024] 
-#> peak picking: SuperSmoother noise estimation and kNeighbors centroid m/z refinement on spectra of MS level(s)2 [Wed May  1 08:23:06 2024] 
-#> peak picking: MAD noise estimation and kNeighbours centroid m/z refinement on spectra of MS level(s)2 [Wed May  1 08:23:06 2024] 
-#> peak picking: SuperSmoother noise estimation and descendPeak centroid m/z refinement on spectra of MS level(s)2 [Wed May  1 08:23:06 2024] 
-#> Spectra centroided: Wed May  1 08:23:06 2024 
+#> peak picking: MAD noise estimation and none centroid m/z refinement on spectra of MS level(s)2 [Wed May 15 16:30:33 2024] 
+#> peak picking: SuperSmoother noise estimation and kNeighbors centroid m/z refinement on spectra of MS level(s)2 [Wed May 15 16:30:33 2024] 
+#> peak picking: MAD noise estimation and kNeighbours centroid m/z refinement on spectra of MS level(s)2 [Wed May 15 16:30:33 2024] 
+#> peak picking: SuperSmoother noise estimation and descendPeak centroid m/z refinement on spectra of MS level(s)2 [Wed May 15 16:30:33 2024] 
+#> Spectra centroided: Wed May 15 16:30:33 2024 
 #>  MSnbase version: 1.1.22 
 
 
@@ -235,22 +219,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/plot-methods.html b/reference/plot-methods.html index 30c59781..00a0a3ee 100644 --- a/reference/plot-methods.html +++ b/reference/plot-methods.html @@ -1,6 +1,5 @@ Plotting 'MSnExp' and 'Spectrum' object(s) — plot-methods • MSnbase - -
    - - -

    Plotting 'MSnExp' and 'Spectrum' object(s)

    -
    -
    - -

    These methods provide the functionality to plot mass spectrometry data provided as MSnExp, OnDiskMSnExp or Spectrum @@ -113,58 +100,38 @@

    Plotting 'MSnExp' and 'Spectrum' object(s)

    expected fragement ions are calculated and matched/annotated on the spectum plot.

    - -

    Arguments

    x

    Objects of class "Spectrum", "Spectrum2" or "MSnExp" to be plotted.

    - -
    y

    Missing, "Spectrum" or "character".

    - -
    reporters

    An object of class "ReporterIons" that defines the peaks to be plotted. If not specified, full must be set to 'TRUE'.

    - -
    full

    Logical indicating whether full spectrum (respectively spectra) of only reporter ions of interest should be plotted. Default is 'FALSE', in which case reporters must be defined.

    - -
    centroided.

    Logical indicating if spectrum or spectra are in centroided mode, in which case peaks are plotted as histograms, rather than curves.

    - -
    plot

    Logical specifying whether plot should be printed to current device. Default is 'TRUE'.

    - -
    w1

    Width of sticks for full centroided spectra. Default is to use maximum MZ value divided by 500.

    - -
    w2

    Width of histogram bars for centroided reporter ions plots. Default is 0.01.

    - -

    See below for more details.

    - -

    Methods

    @@ -172,7 +139,6 @@

    Methods

    type = c("spectra", "XIC"), reporters = "ReporterIons", full = "logical", plot = "logical", ...)
    -

    For type = "spectra": Plots all the spectra in the MSnExp object vertically. One of reporters must be defined or full set to 'TRUE'. In case of MSnExp @@ -190,49 +156,36 @@

    Methods

    and filterMz functions to narrow on an ion of interest. See examples below. This plot uses base R plotting. Additional arguments to the plot function can be - passed with ....

    + passed with ....

    Additional arguments for type = "XIC" are:

    col

    color for the border of the points. Defaults to col = "grey".

    - -
    colramp

    color function/ramp to be used for the intensity-dependent background color of data points. Defaults to colramp = topo.colors.

    - -
    grid.color

    color for the grid lines. Defaults to grid.color = "lightgrey"; use grid.color = NA to disable grid lines altogether.

    - -
    pch

    point character. Defaults to pch = 21

    . -
    ...

    additional parameters for the low-level plot function.

    - - -

    -
    plot(signature(x = "Spectrum", y = "missing"), reporters = "ReporterIons", full = "logical", centroided. = "logical", plot = "logical", w1, w2)

    Displays the MZs against intensities of - the Spectrum object as a line plot. + the Spectrum object as a line plot. At least one of reporters being defined or full - set to 'TRUE' is required. + set to 'TRUE' is required. reporters and full are used only for "Spectrum2" objects. Full "Spectrum1" spectra are plotted by default.

    - -
    plot(signature(x = "Spectrum2", y = "character"), orientation = "numeric", add = "logical", col = "character", pch, xlab = "character", ylab = "character", xlim = "numeric", ylim = @@ -251,9 +204,6 @@

    Methods

    fragments=MSnbase:::calculateFragments_Spectrum2 and fragments.cex=0.75. Additional arguments ... are passed to plot.default.

    - - -

    See also

    @@ -266,7 +216,6 @@

    See also

    Author

    Laurent Gatto <lg390@cam.ac.uk>, Johannes Rainer and Sebastian Gibb

    -

    Examples

    data(itraqdata)
@@ -304,22 +253,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/plot2d-methods.html b/reference/plot2d-methods.html index 0b2c8c98..6148a54c 100644 --- a/reference/plot2d-methods.html +++ b/reference/plot2d-methods.html @@ -8,8 +8,6 @@ - -
    - - -

    The 'plot2d' method for 'MSnExp' quality assessment

    -
    -

    These methods plot the retention time vs. precursor MZ for the whole "MSnExp" experiment. Individual dots will be @@ -83,8 +73,6 @@

    The 'plot2d' method for 'MSnExp' quality assessment

    The methods make use the ggplot2 system. An object of class 'ggplot' is returned invisibly.

    - -

    Arguments

    object
    @@ -94,31 +82,24 @@

    Arguments

    'file', 'peaks.count' or 'charge', depending on the z parameter. Such a data frame is typically generated using the header method on "MSnExp" object.

    -
    z

    A character indicating according to what variable to colour the dots. One of, possibly abreviated, "ionCount" (total ion count), "file" (raw data file), "peaks.count" (peaks count) or "charge" (precursor charge).

    -
    alpha

    Numeric [0,1] indicating transparence level of points.

    -
    plot

    A logical indicating whether the plot should be printed (default is 'TRUE').

    -

    Methods

    signature(object = "MSnExp", ...)

    Plots a 'MSnExp' summary.

    -
    signature(object = "data.frame", ...)

    Plots a summary of the 'MSnExp' experiment described by the data frame.

    - -

    See also

    @@ -129,7 +110,6 @@

    See also

    Author

    Laurent Gatto <lg390@cam.ac.uk>

    -

    Examples

    itraqdata
@@ -170,22 +150,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/plotDensity-methods.html b/reference/plotDensity-methods.html index 68e7745b..cc44a5c2 100644 --- a/reference/plotDensity-methods.html +++ b/reference/plotDensity-methods.html @@ -1,14 +1,12 @@ The 'plotDensity' method for 'MSnExp' quality assessment — plotDensity-methods • MSnbase - -
    - - -

    The 'plotDensity' method for 'MSnExp' quality assessment

    -
    -

    These methods plot the distribution of several parameters of interest for the different precursor charges for "MSnExp" - experiment.

    + experiment.

    The methods make use the ggplot2 system. An object of class 'ggplot' is returned invisibly.

    - -

    Arguments

    object
    @@ -92,31 +80,24 @@

    Arguments

    depending on the z parameter. Such a data frame is typically generated using the header method on "MSnExp" object.

    -
    z

    A character indicating which parameter's densitiy to plot. One of, possibly abreviated, "ionCount" (total ion count), "peaks.count" (peaks count) or "precursor.mz" (precursor MZ).

    -
    log

    Logical, whether to log transform the data (default is 'FALSE').

    -
    plot

    A logical indicating whether the plot should be printed (default is 'TRUE').

    -

    Methods

    signature(object = "MSnExp", ...)

    Plots a 'MSnExp' summary.

    -
    signature(object = "data.frame", ...)

    Plots a summary of the 'MSnExp' experiment described by the data frame.

    - -

    See also

    @@ -127,7 +108,6 @@

    See also

    Author

    Laurent Gatto <lg390@cam.ac.uk>

    -

    Examples

    itraqdata
@@ -171,22 +151,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/plotMzDelta-methods.html b/reference/plotMzDelta-methods.html index 5904be03..9f6d3217 100644 --- a/reference/plotMzDelta-methods.html +++ b/reference/plotMzDelta-methods.html @@ -19,7 +19,7 @@ Note that figures in Foster et al 2011 have been produced and optimised for centroided data. Application of the plot as is for data in profile mode has not been tested thoroughly, although the example - below suggest that it might work. + below suggest that it might work. The methods make use the ggplot2 system. An object of class ggplot is returned invisibly. Most of the code for plotMzDelta has kindly been contributed by @@ -27,8 +27,6 @@ - -
    - - -

    The delta m/z plot

    -
    -

    The m/z delta plot illustrates the suitability of MS2 spectra for identification by plotting the m/z differences of the most intense @@ -115,80 +105,64 @@

    The delta m/z plot

    Note that figures in Foster et al 2011 have been produced and optimised for centroided data. Application of the plot as is for data in profile mode has not been tested thoroughly, although the example - below suggest that it might work.

    + below suggest that it might work.

    The methods make use the ggplot2 system. An object of class ggplot is returned invisibly.

    Most of the code for plotMzDelta has kindly been contributed by Guangchuang Yu.

    - -

    Arguments

    object

    An object of class MSnExp or mzRramp (from the mzR package) containing MS2 spectra.

    -
    reporters

    An object of class class "ReporterIons" that defines which reporter ion peaks to set to 0. The default value NULL leaves the spectra as they are.

    -
    subset
    -

    A numeric between 0 and 1 to use a subset of +

    A numeric between 0 and 1 to use a subset of object's MS2 spectra.

    -
    percentage

    The percentage of most intense peaks to be used for the plot. Default is 0.1.

    -
    precMz

    A numeric of length one or NULL default. In the latter (and preferred) case, the precursor m/z values are extracted from the individual MS2 spectra using the precursorMz method.

    -
    precMzWidth
    -

    A numeric of length 1 that specifies the +

    A numeric of length 1 that specifies the width around the precursor m/z where peaks are set to 0. Default is 2.

    -
    bw

    A numeric specifying the bandwith to be used to bin the delta m/z value to plot the histogram. Default if 1. See geom_histogram for more details.

    -
    xlim

    A numeric of length 2 specifying the range of delta m/z to plot on the histogram. Default is c(40,200).

    -
    withLabels

    A logical defining if amino acid residue labels are plotted on the figure. Default is TRUE.

    -
    size

    A numeric of length 1 specifying the font size of amino acids lables. Default is 2.5.

    -
    plot

    A logical of length 1 that defines whether the figure should be plotted on the active device. Default is TRUE. Note that the ggplot object is always returned invisibly.

    -
    verbose

    A logical of length 1 specifying whether textual output and a progress bar illustration the progress of data processing should be printed. Default is TRUE

    -

    Methods

    signature(object = "MSnExp", ...)

    Plots and (invisibly) returns the m/z delta histogram.

    - -

    See also

    @@ -207,7 +181,6 @@

    References

    Author

    Laurent Gatto <lg390@cam.ac.uk> and Guangchuang Yu

    -

    Examples

    mzdplot <- plotMzDelta(itraqdata,
@@ -243,22 +216,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/plotNA-methods.html b/reference/plotNA-methods.html index e875890d..1050bb84 100644 --- a/reference/plotNA-methods.html +++ b/reference/plotNA-methods.html @@ -12,8 +12,6 @@ - -
    - - -

    Exploring missing data in 'MSnSet' instances

    -
    -

    These methods produce plots that illustrate missing data.

    is.na returns the expression matrix of it MSnSet @@ -91,8 +81,6 @@

    Exploring missing data in 'MSnSet' instances

    The methods make use the ggplot2 system. An object of class 'ggplot' is returned invisibly.

    - -

    Methods

    is.na
    @@ -100,7 +88,6 @@

    Methods

    Returns the a matrix of logicals of dimensions dim(x) specifiying if respective values are missing in the MSnSet's expression matrix.

    -
    plotNA

    signature(object = "MSnSet", pNA = "numeric") Plots missing data for an MSnSet instance. pNA is a @@ -109,8 +96,6 @@

    Methods

    highlighted with a point on the figure, illustrating the overall percentage of NA values in the full data set and the number of proteins retained. Default is 1/2.

    - -

    Author

    @@ -121,7 +106,6 @@

    See also

    See also the filterNA method to filter out features with a specified proportion if missing values.

    -

    Examples

    data(msnset)
@@ -151,22 +135,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/plotSpectrumSpectrum-methods.html b/reference/plotSpectrumSpectrum-methods.html index 06691c52..42ca6d93 100644 --- a/reference/plotSpectrumSpectrum-methods.html +++ b/reference/plotSpectrumSpectrum-methods.html @@ -7,8 +7,6 @@ - -
    - - -

    Plotting a 'Spectrum' vs another 'Spectrum' object.

    -
    -

    These method plot mass spectra MZ values against the intensities as line plots. The first spectrum is plotted in the upper panel and the other in @@ -81,19 +71,14 @@

    Plotting a 'Spectrum' vs another 'Spectrum' object.

    colour. If a peptide sequence is provided it automatically calculates and labels the fragments.

    - -

    Arguments

    x

    Object of class "Spectrum" .

    -
    y

    Object of class "Spectrum" .

    -
    ...

    Further arguments passed to internal functions.

    -

    Methods

    @@ -127,8 +112,6 @@

    Methods

    peaks.cex=0.5 of the peaks. The size of the fragment/legend labels could be set using fragments.cex=0.75 or legend.cex respectively. See par for details about graphical parameters in general.

    - -

    Author

    @@ -139,7 +122,6 @@

    See also

    More spectrum plotting available in plot.Spectrum.

    More details about fragment calculation: calculateFragments.

    -

    Examples

    ## find path to a mzXML file
@@ -179,22 +161,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/precSelection.html b/reference/precSelection.html index a7f85abe..70955bdf 100644 --- a/reference/precSelection.html +++ b/reference/precSelection.html @@ -12,8 +12,6 @@ - -
    - - -

    Number of precursor selection events

    -
    -

    precSelection computes the number of selection events each precursor ions has undergone in an tandem MS experiment. This will be @@ -91,25 +81,19 @@

    Number of precursor selection events

    precSelectionTable is a wrapper around precSelection and returns a table with the number of single, 2-fold, ... selection events.

    - 
    precSelection(object,n)
    -

    Arguments

    object

    An instane of class "MSnExp".

    -
    n

    The number of decimal places to round the precursor MZ to. Is passed to the round function.

    -

    Value

    - -

    A named integer in case of precSelection and a table for

    precSelectionTable.

    @@ -118,7 +102,6 @@

    Value

    Author

    Laurent Gatto <lg390@cam.ac.uk>

    -

    Examples

    precSelection(itraqdata)
@@ -167,22 +150,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/purityCorrect-methods.html b/reference/purityCorrect-methods.html index 3ddde614..5d0fe2fa 100644 --- a/reference/purityCorrect-methods.html +++ b/reference/purityCorrect-methods.html @@ -31,8 +31,6 @@ - -
    - - -

    Performs reporter ions purity correction

    -
    -

    Manufacturers sometimes provide purity correction values indicating the percentages of each reporter ion that have masses differing by @@ -129,20 +119,15 @@

    Performs reporter ions purity correction

    If edit = TRUE, the the matrix can be edited before it is returned.

    - -

    Methods

    signature(object = "MSnSet", impurities = "matrix")

    - -

    Arguments

    object

    An object of class "MSnSet".

    -
    impurities

    A square 'matrix' of dim equal to ncol(object) defining the correction coefficients to be applied. @@ -163,9 +148,7 @@

    Arguments

    .126127N127C128N128C129N129C130N130C131
    % reporter 1260.9500.0000.0500.0000.0000.0000.0000.0000.0000.000
    % reporter 127N0.0000.9400.0000.0580.0000.0000.0000.0000.0000.000
    % reporter 127C0.0030.0000.9490.0000.0480.0000.0000.0000.0000.000
    % reporter 128N0.0000.0040.0000.9550.0000.0410.0000.0000.0000.000
    % reporter 128C0.0000.0000.0060.0000.9640.0000.0300.0000.0000.000
    % reporter 129N0.0000.0000.0000.0080.0000.9570.0000.0350.0000.000
    % reporter 129C0.0000.0000.0000.0000.0140.0000.9620.0000.0240.000
    % reporter 130N0.0000.0000.0000.0010.0000.0150.0000.9280.0000.024
    % reporter 130C0.0000.0000.0000.0000.0000.0000.0170.0000.9650.000
    % reporter 1310.0000.0000.0000.0000.0000.0020.0000.0200.0000.956

    These examples are provided as defaults impurity correction matrices in makeImpuritiesMatrix.

    -
    -

    Examples

    ## quantifying full experiment
@@ -198,7 +181,7 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> iTRAQ4 quantification by trapezoidation: Wed Apr  1 21:41:53 2015 
-#> Purity corrected: Wed May  1 08:23:15 2024 
+#> Purity corrected: Wed May 15 16:30:43 2024 
 #>  MSnbase version: 1.1.22 
 
 ## default impurity matrix for iTRAQ 8-plex
@@ -233,22 +216,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/quantify-methods.html b/reference/quantify-methods.html index 5c898664..71a262bf 100644 --- a/reference/quantify-methods.html +++ b/reference/quantify-methods.html @@ -14,8 +14,6 @@ - -
    - - -

    Quantifies 'MSnExp' and 'Spectrum' objects

    -
    -

    This method quantifies individual "Spectrum" objects or full "MSnExp" experiments. Current, @@ -95,15 +85,11 @@

    Quantifies 'MSnExp' and 'Spectrum' objects

    BiocParallel package and controlled by the BPPARAM argument.

    - -

    Arguments

    object

    An instance of class "Spectrum" (isobaric tagging only) or "MSnExp".

    - -
    method

    Peak quantitation method. For isobaric tags, one of, possibly abreviated "trapezoidation", "max", or @@ -119,13 +105,9 @@

    Arguments

    as input to combineFeatures to implement spectra counting.

    - -
    reporters

    An instance of class "ReporterIons" that defines the peak(s) to be quantified. For isobaric tagging only.

    - -
    strict

    For isobaric tagging only. If strict is FALSE (default), the quantitation is performed using data points along the entire width @@ -133,8 +115,6 @@

    Arguments

    identified, only data points within apex +/- width of reporter (see "ReporterIons") are used for quantitation.

    - -
    BPPARAM

    Support for parallel processing using the BiocParallel infrastructure. When missing (default), the default registered @@ -143,34 +123,20 @@

    Arguments

    BiocParallelParam parameter instance: SnowParam, MulticoreParam, DoparParam, ... see the BiocParallel package for details.

    - -
    parallel

    Deprecated. Please see BPPARAM.

    - -
    qual

    Should the qual slot be populated. Default is TRUE.

    - -
    pepseq

    A character giving the peptide sequence column in the feature data. Default is "sequence".

    - - -
    verbose

    Verbose of the output (only for MSnExp objects).

    - -
    ...

    Further arguments passed to the quantitation functions.

    -

    Details

    - -

    "ReporterIons" define specific MZ at which peaks are expected and a window around that MZ value. A peak of interest is searched for in that window. Since version 1.1.2, warnings are not @@ -198,7 +164,6 @@

    Methods

    signature(object = "MSnExp", method = "character", reporters = "ReporterIons", verbose = "logical", ...)
    -

    For isobaric tagging, quantifies peaks defined in reporters using method in all spectra of the MSnExp object. If verbose is set to TRUE, a progress bar will be displayed.

    @@ -214,12 +179,9 @@

    Methods

    containing the quantified feature expression and all meta data inherited from the MSnExp object argument.

    - -
    signature(object = "Spectrum", method = "character", reporters = "ReporterIons")
    -

    Quantifies peaks defined in reporters using method in the Spectrum object (isobaric tagging only).

    A list of length 2 will be returned. The first element, named @@ -235,13 +197,9 @@

    Methods

    ('reporter') and precursor MZ value ('precursor') when available.

    - -

    References

    - -

    For details about the spectral index (SI), see Griffin NM, Yu J, Long F, Oh P, Shore S, Li Y, Koziol JA, Schnitzer JE. Label-free, normalized quantification of complex mass spectrometry data for @@ -259,7 +217,6 @@

    Author

    Laurent Gatto <lg390@cam.ac.uk> and Sebastian Gibb <mail@sebastiangibb.de>

    -

    Examples

    
@@ -284,7 +241,7 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> Updated from version 0.3.0 to 0.3.1 [Fri Jul  8 20:23:25 2016] 
-#> iTRAQ4 quantification by trapezoidation: Wed May  1 08:23:16 2024 
+#> iTRAQ4 quantification by trapezoidation: Wed May 15 16:30:44 2024 
 #>  MSnbase version: 1.1.22 
 
 ## specifying a custom parallel framework
@@ -321,12 +278,12 @@ 
    Examples
    
 si <- quantify(msexp, method = "SIn")
 processingData(si)
 #> - - - Processing information - - -
-#> Data loaded: Wed May  1 08:23:17 2024 
-#> Filtered 2 unidentified peptides out [Wed May  1 08:23:17 2024] 
-#> Quantitation by total ion current [Wed May  1 08:23:17 2024] 
-#> Combined 3 features into 3 using sum: Wed May  1 08:23:17 2024 
-#> Quantification by SIn [Wed May  1 08:23:17 2024] 
-#>  MSnbase version: 2.31.0 
+#> Data loaded: Wed May 15 16:30:45 2024 
+#> Filtered 2 unidentified peptides out [Wed May 15 16:30:45 2024] 
+#> Quantitation by total ion current [Wed May 15 16:30:45 2024] 
+#> Combined 3 features into 3 using sum: Wed May 15 16:30:45 2024 
+#> Quantification by SIn [Wed May 15 16:30:45 2024] 
+#>  MSnbase version: 2.31.1 
 exprs(si)
 #>         dummyiTRAQ.mzXML
 #> ECA0510     0.0006553518
@@ -336,13 +293,13 @@ 
    Examples
    
 saf <- quantify(msexp, method = "NSAF")
 processingData(saf)
 #> - - - Processing information - - -
-#> Data loaded: Wed May  1 08:23:17 2024 
-#> Filtered 2 unidentified peptides out [Wed May  1 08:23:17 2024] 
-#> Filtered 0 unidentified peptides out [Wed May  1 08:23:17 2024] 
-#> Quantitation by count [Wed May  1 08:23:17 2024] 
-#> Combined 3 features into 3 using user-defined function: Wed May  1 08:23:17 2024 
-#> Quantification by NSAF [Wed May  1 08:23:17 2024] 
-#>  MSnbase version: 2.31.0 
+#> Data loaded: Wed May 15 16:30:45 2024 
+#> Filtered 2 unidentified peptides out [Wed May 15 16:30:45 2024] 
+#> Filtered 0 unidentified peptides out [Wed May 15 16:30:45 2024] 
+#> Quantitation by count [Wed May 15 16:30:45 2024] 
+#> Combined 3 features into 3 using user-defined function: Wed May 15 16:30:45 2024 
+#> Quantification by NSAF [Wed May 15 16:30:45 2024] 
+#>  MSnbase version: 2.31.1 
 exprs(saf)
 #>         dummyiTRAQ.mzXML
 #> ECA0510        0.4306167
@@ -356,22 +313,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/readMSData.html b/reference/readMSData.html index 217e9f2f..88883f0f 100644 --- a/reference/readMSData.html +++ b/reference/readMSData.html @@ -6,8 +6,6 @@ - -
    - - -
    @@ -72,14 +64,12 @@

    Imports mass-spectrometry raw data files as 'MSnExp' instances.

    Source: R/readMSData.R
    -

    Reads as set of XML-based mass-spectrometry data files and generates an MSnExp object. This function uses the functionality provided by the mzR package to access data and meta data in mzData, mzXML and mzML.

    - 
    readMSData(
   files,
@@ -92,31 +82,22 @@ 
    Imports mass-spectrometry raw data files as 'MSnExp' instances.
    
   mode = c("inMemory", "onDisk")
 )
    -

    Arguments

    files

    A character with file names to be read and parsed.

    - -
    pdata

    An object of class AnnotatedDataFrame or NULL (default).

    - -
    msLevel.

    MS level spectra to be read. In inMemory mode, use 1 for MS1 spectra or any larger numeric for MSn spectra. Default is 2 for InMemory mode. onDisk mode supports multiple levels and will, by default, read all the data.

    - -
    verbose

    Verbosity flag. Default is to use isMSnbaseVerbose().

    - -
    centroided.

    A logical, indicating whether spectra are centroided or not. Default is NA in which case the information @@ -125,30 +106,21 @@

    Arguments

    vector of logicals, where the first element is for MS1, the second element is for MS2, ... See OnDiskMSnExp for an example.

    - -
    smoothed.

    A logical indicating whether spectra already smoothed or not. Default is NA.

    - -
    cache.

    Numeric indicating caching level. Default is 0 for MS1 and 1 MS2 (or higher). Only relevant for inMemory mode.

    - -
    mode

    On of "inMemory" (default) or "onDisk". The former loads the raw data in memory, while the latter only generates the object and the raw data is accessed on disk when needed. See the benchmarking vignette for memory and speed implications.

    -

    Value

    - -

    An MSnExp object for inMemory mode and a OnDiskMSnExp object for onDisk mode.

    @@ -178,7 +150,6 @@

    See also

    Author

    Laurent Gatto

    -

    Examples

    file <- dir(system.file(package = "MSnbase", dir = "extdata"),
@@ -193,8 +164,8 @@ 
    Examples
    
 #>  Number of spectra: 5 
 #>  MSn retention times: 25:01 - 25:02 minutes
 #> - - - Processing information - - -
-#> Data loaded: Wed May  1 08:23:19 2024 
-#>  MSnbase version: 2.31.0 
+#> Data loaded: Wed May 15 16:30:46 2024 
+#>  MSnbase version: 2.31.1 
 #> - - - Meta data  - - -
 #> phenoData
 #>   rowNames: dummyiTRAQ.mzXML
@@ -217,8 +188,8 @@ 
    Examples
    
 #>  Number of spectra: 5 
 #>  MSn retention times: 25:01 - 25:02 minutes
 #> - - - Processing information - - -
-#> Data loaded [Wed May  1 08:23:19 2024] 
-#>  MSnbase version: 2.31.0 
+#> Data loaded [Wed May 15 16:30:47 2024] 
+#>  MSnbase version: 2.31.1 
 #> - - - Meta data  - - -
 #> phenoData
 #>   rowNames: dummyiTRAQ.mzXML
@@ -239,22 +210,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/readMSnSet.html b/reference/readMSnSet.html index 227de197..bd0a3b6c 100644 --- a/reference/readMSnSet.html +++ b/reference/readMSnSet.html @@ -1,6 +1,5 @@ Read 'MSnSet' — readMSnSet • MSnbase - -
    - - -

    Read 'MSnSet'

    -
    -
    - -

    This function reads data files to generate an MSnSet instance. It is a wrapper around Biobase's readExpressionSet function with an @@ -97,7 +84,6 @@

    Read 'MSnSet'

    rownames as additional argument to defined feature names. It is ignored and used to set fnames if not provided otherwise.

    - 
    readMSnSet(exprsFile,
            phenoDataFile,
@@ -118,12 +104,8 @@ 
    Read 'MSnSet'
    
 
 readMSnSet2(file, ecol, fnames, ...)
    -

    Arguments

    - - -

    Arguments direclty passed to readExpressionSet. The description is from the readExpressionSet documentation page.

    exprsFile
    @@ -132,71 +114,55 @@

    Arguments

    features and columns as samples. read.table is called with this as its file argument and further arguments given by exprsArgs.

    -
    phenoDataFile

    (character) File or connection from which to read phenotypic data. read.AnnotatedDataFrame is called with this as its file argument and further arguments given by phenoDataArgs.

    -
    experimentDataFile

    (character) File or connection from which to read experiment data. read.MIAME is called with this as its file argument and further arguments given by experimentDataArgs.

    -
    notesFile

    (character) File or connection from which to read notes; readLines is used to input the file.

    -
    path

    (optional) directory in which to find all the above files.

    -
    annotation

    (character) A single character string indicating the annotation associated with this ExpressionSet.

    -
    exprsArgs

    A list of arguments to be used with read.table when reading in the expression matrix.

    -
    phenoDataArgs

    A list of arguments to be used (with read.AnnotatedDataFrame) when reading the phenotypic data.

    -
    experimentDataArgs

    A list of arguments to be used (with read.MIAME) when reading the experiment data.

    -
    sep, header, quote, stringsAsFactors, row.names

    arguments used by the read.table-like functions.

    -
    widget

    A boolean value indicating whether widgets can be used. Widgets are NOT yet implemented for read.AnnotatedDataFrame.

    -
    ...

    Further arguments that can be passed on to the read.table-like functions.

    - -

    Additional argument, specific to readMSnSet:

    featureDataFile

    (character) File or connection from which to read feature data. read.AnnotatedDataFrame is called with this as its file argument and further arguments given by phenoDataArgs.

    -
    featureDataArgs

    A list of arguments to be used (with read.AnnotatedDataFrame) when reading the phenotypic data.

    - -

    Arguments for readMSnSet2:

    file

    A character indicating the spreadsheet file or a @@ -208,10 +174,7 @@

    Arguments

    spreadsheet is in Excel format. The appropriate sheet can first be read into R as a data.frame using, for example readxl::read_excel, and then pass it to readMSnSet2.

    -

    - -
    ecol

    A numeric indicating the indices of the columns to be used as expression values. Can also be a character @@ -220,14 +183,9 @@

    Arguments

    - that will be converted to a .. If ecol does not match, the error message will dislpay the column names are see by R.

    - - -
    fnames

    An optional character or numeric of length 1 indicating the column to be used as feature names.

    - -

    Value

    @@ -240,13 +198,11 @@

    Author

    See also

    -

    The grepEcols and getEcols helper functions to identify the ecol values. The MSnbase-io vignette illustrates these functions in detail. It can be accessed with vignette("MSnbase-io").

    -

    Examples

    if (FALSE) {
@@ -277,7 +233,7 @@ 
    Examples
    
 #> experimentData: use 'experimentData(object)'
 #> Annotation:  
 #> - - - Processing information - - -
-#>  MSnbase version: 2.31.0 
+#>  MSnbase version: 2.31.1 
 head(exprs(res)) ## columns 5 to 20
 #>      M1F1A    M1F4A    M1F7A   M1F11A    M1F2B    M1F5B    M1F8B   M1F11B
 #> 1 0.323250 0.275500 0.216000 0.185250 0.465667 0.199667 0.174333 0.160333
@@ -308,22 +264,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/readMgfData.html b/reference/readMgfData.html index a52cb08e..9576da1c 100644 --- a/reference/readMgfData.html +++ b/reference/readMgfData.html @@ -4,8 +4,6 @@ - -
    - - -

    Import mgf files as 'MSnExp' instances.

    -
    -

    Reads a mgf file and generates an "MSnExp" object.

    - 
    readMgfData(filename, pdata = NULL, centroided = TRUE, smoothed = FALSE,
 verbose = isMSnbaseVerbose(), cache = 1)
    -

    Arguments

    filename

    character vector with file name to be read.

    -
    pdata

    an object of class "AnnotatedDataFrame".

    -
    smoothed

    Logical indicating whether spectra already smoothed or not. Default is 'FALSE'. Used to initialise "MSnProcess" object in processingData slot.

    -
    centroided

    Logical indicating whether spectra are centroided or not. Default is 'TRUE'. Used to initialise "MSnProcess" object in processingData slot.

    -
    cache

    Numeric indicating caching level. Default is 1. Under development.

    -
    verbose

    verbosity flag.

    -

    Value

    - -

    An instance of

    @@ -131,7 +111,6 @@

    See also

    objects to mgf files. Raw data files can also be read with the readMSData function.

    -

    Examples

      data(itraqdata)
@@ -168,8 +147,8 @@ 
    Examples
    
 #>  Number of spectra: 3 
 #>  MSn retention times: 17:08 - 18:47 minutes
 #> - - - Processing information - - -
-#> Data loaded: Wed May  1 08:23:21 2024 
-#>  MSnbase version: 2.31.0 
+#> Data loaded: Wed May 15 16:30:49 2024 
+#>  MSnbase version: 2.31.1 
 #> - - - Meta data  - - -
 #> phenoData
 #>   rowNames: 1
@@ -209,22 +188,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/readMzIdData.html b/reference/readMzIdData.html index dccf3f32..507ac25e 100644 --- a/reference/readMzIdData.html +++ b/reference/readMzIdData.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,29 +62,21 @@

    Import peptide-spectrum matches

    Source: R/functions-addIdentificationData.R
    -

    Reads as set of mzId files containing PSMs an generates a data.frame.

    - 
    readMzIdData(files)
    -

    Arguments

    files

    A character of mzid files.

    -

    Value

    - -

    A data.frame containing the PSMs stored in the mzId

    - -

    files.

    @@ -109,7 +93,6 @@

    See also

    Author

    Laurent Gatto

    -

    Examples

    idf <- "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid"
@@ -34421,22 +34404,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/readMzTabData.html b/reference/readMzTabData.html index a511200e..3c17b819 100644 --- a/reference/readMzTabData.html +++ b/reference/readMzTabData.html @@ -6,8 +6,6 @@ - -
    - - -
    @@ -72,14 +64,12 @@

    Read an 'mzTab' file

    Source: R/readWriteMzTab.R
    -

    This function can be used to create an "MSnSet" by reading and parsing an mzTab file. The metadata section is always used to populate the MSnSet's experimentData()@other$mzTab slot.

    - 
    readMzTabData(
   file,
@@ -88,36 +78,26 @@ 
    Read an 'mzTab' file
    
   verbose = isMSnbaseVerbose()
 )
    -

    Arguments

    file

    A character with the mzTab file to be read in.

    - -
    what

    One of "PRT", "PEP" or "PSM", defining which of protein, peptide PSMs section should be returned as an MSnSet.

    - -
    version

    A character defining the format specification version of the mzTab file. Default is "1.0". Version "0.9" is available of backwards compatibility. See readMzTabData_v0.9 for details.

    - -
    verbose

    Produce verbose output.

    -

    Value

    - -

    An instance of class MSnSet.

    @@ -129,7 +109,6 @@

    See also

    Author

    Laurent Gatto

    -

    Examples

    testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/examples/1_0-Proteomics-Release/PRIDE_Exp_Complete_Ac_16649.xml-mztab.txt"
@@ -150,7 +129,7 @@ 
    Examples
    
 #>   pubMedIds: pubmed:21398567 
 #> Annotation:  
 #> - - - Processing information - - -
-#>  MSnbase version: 2.31.0 
+#>  MSnbase version: 2.31.1 
 
 head(fData(prot))
 #>            accession
@@ -249,7 +228,7 @@ 
    Examples
    
 #>   pubMedIds: pubmed:21398567 
 #> Annotation:  
 #> - - - Processing information - - -
-#>  MSnbase version: 2.31.0 
+#>  MSnbase version: 2.31.1 
 
 head(fData(psms))
 #>       sequence PSM_ID accession unique       database database_version
@@ -287,22 +266,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/readMzTabData_v0.9.html b/reference/readMzTabData_v0.9.html index e1af2f22..515f2cbe 100644 --- a/reference/readMzTabData_v0.9.html +++ b/reference/readMzTabData_v0.9.html @@ -6,8 +6,6 @@ - -
    - - -
    @@ -72,40 +64,30 @@

    Read an 'mzTab' file

    Source: R/readWriteMzTab.R
    -

    This function can be used to create a "MSnSet" by reading and parsing an mzTab file. The metadata section is always used to populate the MSnSet's experimentData slot.

    - 
    readMzTabData_v0.9(file, what = c("PRT", "PEP"), verbose = isMSnbaseVerbose())
    -

    Arguments

    file

    A character with the mzTab file to be read in.

    - -
    what

    One of "PRT" or "PEP", defining which of protein of peptide section should be parse. The metadata section, when available, is always used to populate the experimentData slot.

    - -
    verbose

    Produce verbose output.

    -

    Value

    - -

    An instance of class MSnSet.

    @@ -117,7 +99,6 @@

    See also

    Author

    Laurent Gatto

    -

    Examples

    testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/legacy/jmztab-1.0/examples/mztab_itraq_example.txt"
@@ -142,8 +123,8 @@ 
    Examples
    
 #> experimentData: use 'experimentData(object)'
 #> Annotation:  
 #> - - - Processing information - - -
-#> mzTab read: Wed May  1 08:23:29 2024 
-#>  MSnbase version: 2.31.0 
+#> mzTab read: Wed May 15 16:30:57 2024 
+#>  MSnbase version: 2.31.1 
 
 pep <- readMzTabData_v0.9(testfile, "PEP")
 #> Warning: Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details.
@@ -165,8 +146,8 @@ 
    Examples
    
 #> experimentData: use 'experimentData(object)'
 #> Annotation:  
 #> - - - Processing information - - -
-#> mzTab read: Wed May  1 08:23:29 2024 
-#>  MSnbase version: 2.31.0 
+#> mzTab read: Wed May 15 16:30:57 2024 
+#>  MSnbase version: 2.31.1
    @@ -174,22 +155,12 @@

    Examples

    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/readSRMData.html b/reference/readSRMData.html index 14ce80ed..c7afce80 100644 --- a/reference/readSRMData.html +++ b/reference/readSRMData.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,31 +62,23 @@

    Read SRM/MRM chromatographic data

    Source: R/readChromData.R
    -

    The readSRMData function reads MRM/SRM data from provided mzML files and returns the results as a MChromatograms() object.

    - 
    readSRMData(files, pdata = NULL)
    -

    Arguments

    files

    character with the files containing the SRM/MRM data.

    - -
    pdata

    data.frame or AnnotatedDataFrame with file/sample descriptions.

    -

    Value

    - -

    A MChromatograms() object. See details above for more information.

    @@ -128,7 +112,6 @@

    Note

    Author

    Johannes Rainer

    -

    Examples

    
@@ -455,22 +438,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/reduce-data.frame-method.html b/reference/reduce-data.frame-method.html index 33bf39c2..c17a3bd2 100644 --- a/reference/reduce-data.frame-method.html +++ b/reference/reduce-data.frame-method.html @@ -6,8 +6,6 @@ - -
    - - -
    @@ -72,38 +64,28 @@

    Reduce a data.frame

    Source: R/utils.R
    -

    Reduce a data.frame so that the (primary) key column contains only unique entries and other columns pertaining to that entry are combined into semicolon-separated values into a single row/observation.

    - 
    # S4 method for class 'data.frame'
 reduce(x, key, sep = ";")
    -

    Arguments

    x

    A data.frame.

    - -
    key

    The column name (currenly only one is supported) to be used as primary key.

    - -
    sep

    The separator. Default is ;.

    -

    Value

    - -

    A reduced data.frame.

    @@ -117,7 +99,6 @@

    Details

    Author

    Laurent Gatto

    -

    Examples

    dfr <- data.frame(A = c(1, 1, 2),
@@ -166,22 +147,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/removeNoId-methods.html b/reference/removeNoId-methods.html index 673fb7ae..5284eb02 100644 --- a/reference/removeNoId-methods.html +++ b/reference/removeNoId-methods.html @@ -5,8 +5,6 @@ - -
    - - -

    Removes non-identified features

    -
    -

    The method removes non-identifed features in MSnExp and MSnSet instances using relevant information from the feaureData slot of a user-provide filtering vector of logicals.

    - -

    Methods

    signature(object = "MSnExp", fcol = "pepseq", keep = @@ -88,12 +76,9 @@

    Methods

    NA. Alternatively, one can also manually define keep, a vector of logical, defining the feature to be retained.

    -
    signature(object = "MSnSet", fcol = "pepseq", keep = NULL)

    As above of MSnSet instances.

    - -

    Author

    @@ -103,7 +88,6 @@

    Author

    See also

    MSnExp and MSnSet.

    -

    Examples

      quantFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
@@ -162,22 +146,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/removePeaks-methods.html b/reference/removePeaks-methods.html index 8206a518..c26e9f1e 100644 --- a/reference/removePeaks-methods.html +++ b/reference/removePeaks-methods.html @@ -9,15 +9,13 @@ If the spectrum is in profile mode, ranges of successive non-0 peaks &lt;= t are set to 0. If the spectrum is centroided, then individual peaks &lt;= t are set to 0. See the example below for - an illustration. + an illustration. Note that the number of peaks is not changed; the peaks below the threshold are set to 0 and the object is not cleanded out (see clean). An illustrative example is shown below.'> - -
    - - -

    Removes low intensity peaks

    -
    -

    This method sets low intensity peaks from individual spectra (Spectrum instances) or whole experiments (MSnExp @@ -94,13 +84,11 @@

    Removes low intensity peaks

    If the spectrum is in profile mode, ranges of successive non-0 peaks <= t are set to 0. If the spectrum is centroided, then individual peaks <= t are set to 0. See the example below for - an illustration.

    + an illustration.

    Note that the number of peaks is not changed; the peaks below the threshold are set to 0 and the object is not cleanded out (see clean). An illustrative example is shown below.

    - -

    Methods

    signature(object = "MSnExp", t, verbose = "logical" )
    @@ -110,8 +98,6 @@

    Methods

    numeric values are valid. Displays a control bar if verbose set to TRUE (default). Returns a new MSnExp instance.

    - -
    signature(object = "Spectrum", t, msLevel. = "numeric")

    Removes low intensity peaks of Spectrum @@ -122,9 +108,6 @@

    Methods

    cleaning is ignored. Only relevant when called from OnDiskMSnExp and is only relevant for developers.

    Returns a new Spectrum instance.

    - - -

    Author

    @@ -135,7 +118,6 @@

    See also

    clean and trimMz for other spectra processing methods.

    -

    Examples

    int <- c(2, 0, 0, 0, 1, 5, 1, 0, 0, 1, 3, 1, 0, 0, 1, 4, 2, 1)
@@ -173,7 +155,7 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> Updated from version 0.3.0 to 0.3.1 [Fri Jul  8 20:23:25 2016] 
-#> Curves <= 250000 set to '0': Wed May  1 08:23:33 2024 
+#> Curves <= 250000 set to '0': Wed May 15 16:31:01 2024 
 #>  MSnbase version: 1.1.22 
 
 ## difference between centroided and profile peaks
@@ -203,22 +185,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/removeReporters-methods.html b/reference/removeReporters-methods.html index 764d972c..f6405fb6 100644 --- a/reference/removeReporters-methods.html +++ b/reference/removeReporters-methods.html @@ -3,7 +3,7 @@ spectrum or all the MS2 spectra of an experiment to 0. Reporter data is specified using an "ReporterIons" instance. The peaks are selected around the expected reporter ion - m/z value +/- the reporter width. + m/z value +/- the reporter width. Optionally, the spectrum/spectra can be cleaned to remove successive 0 intensity data points (see the clean function for details). @@ -12,8 +12,6 @@ - -
    - - -

    Removes reporter ion tag peaks

    -
    -

    This methods sets all the reporter tag ion peaks from one MS2 spectrum or all the MS2 spectra of an experiment to 0. Reporter data is specified using an "ReporterIons" instance. The peaks are selected around the expected reporter ion - m/z value +/- the reporter width. + m/z value +/- the reporter width. Optionally, the spectrum/spectra can be cleaned to remove successive 0 intensity data points (see the clean function for details).

    Note that this method only works for MS2 spectra or experiments that contain MS2 spectra. It will fail for MS1 spectrum.

    - -

    Methods

    signature(object = "MSnExp", reporters = "ReporterIons", @@ -104,7 +92,6 @@

    Methods

    value of reporters is NULL, which leaves the spectra as unchanged. The verbose parameter (default is TRUE) defines whether a progress bar should be showed.

    -
    signature(object = "Spectrum", reporters = "ReporterIons", clean = "FALSE")

    The reporter ion peaks defined in the @@ -112,8 +99,6 @@

    Methods

    instance are set to 0 and, if clean is set to TRUE, cleaned. The default value of reporters is NULL, which leaves the spectrum as unchanged.

    - -

    Author

    @@ -124,7 +109,6 @@

    See also

    clean and removePeaks for other spectra processing methods.

    -

    Examples

    sp1 <- itraqdata[[1]]
@@ -150,22 +134,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/selectFeatureData.html b/reference/selectFeatureData.html index a77377b4..ce67ddb5 100644 --- a/reference/selectFeatureData.html +++ b/reference/selectFeatureData.html @@ -6,8 +6,6 @@ - -
    - - -
    @@ -72,51 +64,37 @@

    Select feature variables of interest

    Source: R/fdata-selection.R
    -

    Select feature variables to be retained.

    requiredFvarLabels returns a character vector with the required feature data variable names (fvarLabels, i.e. the column names in the fData data.frame) for the specified object.

    - 
    selectFeatureData(object, graphics = TRUE, fcol)
 
 requiredFvarLabels(x = c("OnDiskMSnExp", "MSnExp", "MSnSet"))
    -

    Arguments

    object

    An MSnSet, MSnExp or OnDiskMSnExp.

    - -
    graphics

    A logical (default is TRUE) indicating whether a shiny application should be used if available. Otherwise, a text menu is used. Ignored if k is not missing.

    - -
    fcol

    A numeric, logical or character of valid feature variables to be passed directly.

    - -
    x

    character(1) specifying the class name for which the required feature data variable names should be returned.

    -

    Value

    - -

    For selectFeatureData: updated object containing only selected feature variables.

    - -

    For requiredFvarLabels: character with the required feature variable names.

    @@ -124,7 +102,6 @@

    Value

    Author

    Laurent Gatto

    -

    Examples

    
@@ -179,22 +156,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/smooth-methods.html b/reference/smooth-methods.html index 8e5b4db6..ac3b763f 100644 --- a/reference/smooth-methods.html +++ b/reference/smooth-methods.html @@ -2,14 +2,12 @@ Smooths 'MSnExp' or 'Spectrum' instances — smooth-methods • MSnbase - -
    - - -

    Smooths 'MSnExp' or 'Spectrum' instances

    -
    -

    This method smooths individual spectra (Spectrum instances) or whole experiments (MSnExp instances). Currently, the Savitzky-Golay-Smoothing (method = "SavitzkyGolay") - and the Moving-Average-Smoothing (method = "MovingAverage") are - available, as implemented in the MALDIquant::smoothIntensity function. + and the Moving-Average-Smoothing (method = "MovingAverage") are + available, as implemented in the MALDIquant::smoothIntensity function. Additional methods might be added at a later stage.

    - -

    Methods

    - -

    signature(x = "MSnExp", method = "character", halfWindowSize = "integer", verbose = "logical", ...)
    -

    Smooths all spectra in MSnExp. method could be "SavitzkyGolay" or "MovingAverage". "halfWindowSize" controls the @@ -113,21 +98,15 @@

    Methods

    polynomial order of the Savitzky-Golay Filter. This method displays a progress bar if verbose = TRUE. Returns an MSnExp instance with smoothed spectra.

    - -
    signature(x = "Spectrum", method = "character", halfWindowSize = "integer", ...)
    -

    Smooths the spectrum (Spectrum instance). This method is the same as above but returns a smoothed Spectrum instead of an MSnExp object. It has no verbose argument. Please read the details for the above MSnExp method.

    - - -

    @@ -136,7 +115,7 @@

    Author

    See also

    -

    clean, pickPeaks, removePeaks and +

    clean, pickPeaks, removePeaks and trimMz for other spectra processing methods.

    @@ -152,7 +131,6 @@

    References

    Bioinformatics 28: 2270-2271. http://strimmerlab.org/software/maldiquant/

    -

    Examples

    sp1 <- new("Spectrum1",
@@ -170,7 +148,7 @@ 
    Examples
    
 #> - - - Processing information - - -
 #> Data loaded: Wed May 11 18:54:39 2011 
 #> Updated from version 0.3.0 to 0.3.1 [Fri Jul  8 20:23:25 2016] 
-#> Spectra smoothed (MovingAverage): Wed May  1 08:23:35 2024 
+#> Spectra smoothed (MovingAverage): Wed May 15 16:31:03 2024 
 #>  MSnbase version: 1.1.22
    @@ -179,22 +157,12 @@

    Examples

    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/trimMz-methods.html b/reference/trimMz-methods.html index 33eed65c..3e0e5855 100644 --- a/reference/trimMz-methods.html +++ b/reference/trimMz-methods.html @@ -1,6 +1,5 @@ Trims 'MSnExp' or 'Spectrum' instances — trimMz-methods • MSnbase - -
    - - -

    Trims 'MSnExp' or 'Spectrum' instances

    -
    -
    - -

    This method selects a range of MZ values in a single spectrum (Spectrum instances) or all the spectra of an experiment (MSnExp instances). The regions to trim are defined by the range of mz argument, such that MZ values <= min(mz) and MZ values >= max(mz) are trimmed away.

    - -

    Methods

    signature(object = "MSnExp", mz = "numeric", msLevel. = @@ -94,8 +79,6 @@

    Methods

    Trims all spectra in MSnExp object according to mz. If msLevel. is defined, then only spectra of that level are trimmer.

    - -
    signature(object = "Spectrum", mz = "numeric", msLevel. = "numeric")

    Trims the Spectrum object and @@ -103,9 +86,6 @@

    Methods

    of the spectrum, and if msLevel(object) != msLevel., cleaning is ignored. Only relevant when called from OnDiskMSnExp and is only relevant for developers.

    - - -

    Author

    @@ -116,7 +96,6 @@

    See also

    removePeaks and clean for other spectra processing methods.

    -

    Examples

    mz <- 1:100
@@ -149,22 +128,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/updateObject-methods.html b/reference/updateObject-methods.html index aab53a2f..7c720435 100644 --- a/reference/updateObject-methods.html +++ b/reference/updateObject-methods.html @@ -1,13 +1,10 @@ Update MSnbase objects — updateObject-methods • MSnbase - -
    - - -

    Update MSnbase objects

    -
    -
    - -

    Methods for function updateObject for objects from the MSnbase package. See updateObject for details.

    - -

    Methods

    signature(object = "MSnExp")

    Update the MSnExp object to the latest class version

    - -
    signature(object = "Spectrum")

    Update the Spectrum object (and it's sub-classes Spectrum1 and Spectrum2) to the latest class version.

    - - -
    -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/writeMSData.html b/reference/writeMSData.html index c37c630e..722492b5 100644 --- a/reference/writeMSData.html +++ b/reference/writeMSData.html @@ -5,8 +5,6 @@ - -
    - - -
    @@ -71,13 +63,11 @@

    Write MS data to mzML or mzXML files

    Source: R/methods-write.R
    -

    The writeMSData,MSnExp and writeMSData,OnDiskMSnExp saves the content of a MSnExp or OnDiskMSnExp object to MS file(s) in either mzML or mzXML format.

    - 
    # S4 method for class 'MSnExp,character'
 writeMSData(
@@ -90,44 +80,30 @@ 
    Write MS data to mzML or mzXML files
    
   software_processing = NULL
 )
    -

    Arguments

    object

    OnDiskMSnExp or MSnExp object.

    - -
    file

    character with the file name(s). Its length has to match the number of samples/files of x.

    - -
    outformat

    character(1) defining the format of the output files. Default output format is "mzml".

    - -
    merge

    logical(1) whether the data should be saved into a single mzML file. Default is merge = FALSE, i.e. each sample is saved to a separate file. Note: merge = TRUE is not yet implemented.

    - -
    verbose

    logical(1) if progress messages should be displayed.

    - -
    copy

    logical(1) if metadata (data processings, original file names etc) should be copied from the original files. See details for more information.

    - -
    software_processing

    optionally provide specific data processing steps. See documentation of the software_processing parameter of mzR::writeMSData().

    -

    Details

    @@ -162,28 +138,17 @@

    Note

    Author

    Johannes Rainer

    -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/writeMgfData-methods.html b/reference/writeMgfData-methods.html index 3b92e6ed..2edbc334 100644 --- a/reference/writeMgfData-methods.html +++ b/reference/writeMgfData-methods.html @@ -2,15 +2,13 @@ Write an experiment or spectrum to an mgf file — writeMgfData-methods • MSnbase - -
    - - -

    Write an experiment or spectrum to an mgf file

    -
    -

    Methods writeMgfData write individual "Spectrum" instances of whole "MSnExp" experiments to a file - in Mascot Generic Format (mgf) (see + in Mascot Generic Format (mgf) (see http://www.matrixscience.com/help/data_file_help.html for more details). Function readMgfData read spectra from and mgf file and creates an "MSnExp" object.

    - -

    Arguments

    object

    An instance of class "Spectrum" or "MSnExp".

    -
    con

    A valid connection or a character string with the name of the file to save the object. In case of the latter, a - file connection is created. If not specified, 'spectrum.mgf' + file connection is created. If not specified, 'spectrum.mgf' or 'experiment.mgf' are used depending on the class of object. Note that existing files are overwritted.

    -
    COM

    Optional character vector with the value for the 'COM' field.

    -
    TITLE

    Optional character vector with the value for the spectrum 'TITLE' field. Not applicable for experiments.

    -

    Methods

    signature(object = "MSnExp")

    Writes the full exeriment to an mgf file.

    -
    signature(object = "Spectrum")

    Writes an individual spectrum to an mgf file.

    - -

    See also

    @@ -132,7 +113,6 @@

    Details

    names will be identical, the spectra are not as a result of the reordering. See example below.

    -

    Examples

    data(itraqdata)
@@ -176,22 +156,12 @@ 
    Examples
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - - diff --git a/reference/writeMzTabData.html b/reference/writeMzTabData.html index 7f08fcbb..3d48d1cc 100644 --- a/reference/writeMzTabData.html +++ b/reference/writeMzTabData.html @@ -4,8 +4,6 @@ - -
    - - -
    @@ -70,12 +62,10 @@

    Export an MzTab object as mzTab file.

    Source: R/readWriteMzTab.R
    -

    writeMzTabData exports an MzTab object as mzTab file. Note that the comment section "COM" are not written out.

    - 
    writeMzTabData(
   object,
@@ -83,49 +73,32 @@ 
    Export an MzTab object as mzTab file.
    
   what = c("MT", "PEP", "PRT", "PSM", "SML", "SMF", "SME")
 )
    -

    Arguments

    object

    MzTab object, either read in by MzTab() or assembled.

    - -
    file

    character(1) with the file name.

    - -
    what

    character with names of the sections to be written out. Expected sections are "MT", "PEP", "PRT", "PSM", "SML", "SMF", or "SME".

    -

    Author

    Steffen Neumann

    -
    - -

    Developed by Laurent Gatto, Johannes Rainer, Sebastian Gibb.

    -

    Site built with pkgdown 2.0.9.9000.

    -
    - - - - - -