refactor: change default for keepAdjustRtime for [,XcmsExperiment

Author: jorainer

NEWS.md

@@ -2,6 +2,8 @@
 
 ## Changes in version 4.7.2
 
+- Change default for `[,XcmsExperiment` and `[,XcmsExperimentHdf5`
+  `keepAdjustedRtime` from `FALSE` to `TRUE`.
 - Fix issue in `[,XcmsExperiment`: the subset operation did not revert the
   retention times of chromatographic peaks with parameter `keepAdjustedRtime =
   FALSE` (issue #801).

R/XcmsExperiment-functions.R

@@ -71,7 +71,7 @@
 #' @noRd
 .subset_xcms_experiment <- function(x, i = integer(),
                                     keepChromPeaks = TRUE,
-                                    keepAdjustedRtime = FALSE,
+                                    keepAdjustedRtime = TRUE,
                                     keepFeatures = FALSE,
                                     ignoreHistory = FALSE,
                                     keepSampleIndex = FALSE, ...) {

R/XcmsExperiment.R

@@ -45,12 +45,12 @@
 #'
 #' - `[`: subset an `XcmsExperiment` by **sample** (parameter `i`). Subsetting
 #'   will by default drop correspondence results (as subsetting by samples will
-#'   obviously affect the feature definition) and alignment results (adjusted
-#'   retention times) while identified chromatographic peaks (for the selected
+#'   obviously affect the feature definition) while alignment results (adjusted
+#'   retention times) and identified chromatographic peaks (for the selected
 #'   samples) will be retained. Which preprocessing results should be
 #'   kept or dropped can also be configured with optional parameters
 #'   `keepChromPeaks` (by default `TRUE`), `keepAdjustedRtime` (by default
-#'   `FALSE`) and `keepFeatures` (by default `FALSE`).
+#'   `TRUE`) and `keepFeatures` (by default `FALSE`).
 #'
 #' - `c()`: multiple `XcmsExperiment` objects can be combined into one using the
 #'   `c()` function. This requires however that all the `XcmsExperiments`'

R/XcmsExperimentHdf5-functions.R

@@ -173,7 +173,7 @@ toXcmsExperiment <- function(object, ...) {
 #' @noRd
 .h5_subset_xcms_experiment <- function(x, i = integer(),
                                        keepChromPeaks = TRUE,
-                                       keepAdjustedRtime = FALSE,
+                                       keepAdjustedRtime = TRUE,
                                        keepFeatures = FALSE,
                                        ignoreHistory = FALSE,
                                        ...) {

R/XcmsExperimentHdf5.R

@@ -69,7 +69,7 @@
 #'
 #' - `[`: subset the `XcmsExperimentHdf5` object to the specified samples.
 #'   Parameters `keepChromPeaks` (default `TRUE`), `keepAdjustedRtime`
-#'   (default `FALSE`) and `keepFeatures` (default `FALSE`) allow to configure
+#'   (default `TRUE`) and `keepFeatures` (default `FALSE`) allow to configure
 #'   whether present chromatographic peaks, alignment or correspondence results
 #'   should be retained. This will only change information in the object (i.e.,
 #'   the reference to the respective entries in the HDF5 file), but will