* Fixes with ggplot in 450K array QC plotting

 * added an option 'differential.report.sites' to decrease runtime by skipping
 the differential site methylation section in the report

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RnBeads@112505 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

@@ -9,8 +9,8 @@ Authors@R: c(
     role = c("aut")),
     person("Fabian", "Mueller", email = "[email protected]",
     role = c("aut", "cre")))
-Date: 2015-12-30
-Version: 1.3.4
+Date: 2016-01-13
+Version: 1.3.5
 Suggests:
     Category,
     GEOquery,

R/main.R

@@ -1360,7 +1360,7 @@ rnb.run.differential <- function(rnb.set, dir.reports,
 	module.start.log("Differential Methylation")
 
 	report <- init.pipeline.report("differential_methylation", dir.reports, init.configuration)
-	optionlist <- rnb.options("analyze.sites","region.types", "differential.permutations", "differential.comparison.columns",
+	optionlist <- rnb.options("analyze.sites", "differential.report.sites", "region.types", "differential.permutations", "differential.comparison.columns",
 		"differential.comparison.columns.all.pairwise","columns.pairing","differential.site.test.method","covariate.adjustment.columns",
 		"differential.adjustment.sva","differential.adjustment.celltype","differential.enrichment")
 	report <- rnb.add.optionlist(report, optionlist)
@@ -1416,7 +1416,7 @@ rnb.run.differential <- function(rnb.set, dir.reports,
 		report <- rnb.add.section(report, "Differential Methylation Analysis", txt)
 	} else {
 		gz <- rnb.getOption("gz.large.files")
-		includeSites <- rnb.getOption("analyze.sites")
+		includeSites <- rnb.getOption("differential.report.sites")
 		report <- rnb.section.diffMeth.introduction(diffmeth,report)
 		if (includeSites){
 			report <- rnb.section.diffMeth.site(rnb.set,diffmeth,report,gzTable=gz)

R/options.R

@@ -720,6 +720,10 @@ rnb.is.option <- function(txt) {
 #'   \item{\bold{\code{differential.enrichment}}\code{ = FALSE}}{
 #'        Flag indicating whether \href{http://www.geneontology.org/}{Gene Ontology} (GO)-enrichment analysis is to be
 #'        conducted on the identified differentially methylated regions.}
+#'   \item{\bold{\code{differential.report.sites}}\code{ = TRUE}}{
+#'        Flag indicating whether a section corresponding to differential site methylation should be added to the report.
+#'        Has no effect on the actual analysis, just the report. To disable differential site methylation analysis entirely
+#'        use the \code{analyze.sites} option.}
 #'   \item{\bold{\code{export.to.bed}}\code{ = TRUE}}{
 #'        Flag indicating whether the data should be exported to bed files.}
 #'   \item{\bold{\code{export.to.trackhub}}\code{ = c("bigBed","bigWig")}}{

inst/NEWS

@@ -1,3 +1,10 @@
+RnBeads 1.3.5
+=============
+
+ * Fixes with ggplot in 450K array QC plotting
+ * added an option 'differential.report.sites' to decrease runtime by skipping
+ the differential site methylation section in the report
+
 RnBeads 1.3.4
 =============
 

inst/extdata/options.txt

@@ -92,6 +92,7 @@ covariate.adjustment.columns	integer.vector	no	yes		NULL
 differential.adjustment.sva	logical	no	no		TRUE
 differential.adjustment.celltype	logical	no	no		TRUE
 differential.enrichment	logical	no	no		FALSE
+differential.report.sites	logical	no	no		TRUE
 export.to.bed	logical	no	no		TRUE
 export.to.trackhub	character.vector	no	yes	(bigBed,bigWig)	(bigBed,bigWig)
 export.to.csv	logical	no	no		FALSE

vignettes/RnBeads.Rnw

@@ -93,7 +93,7 @@
 
 \author{Fabian M\"uller, Yassen Assenov, Pavlo Lutsik \\
 	\small{Contact: \cs{[email protected]}} \\
-	\small{Package version: \cs{1.1.2}}}
+	\small{Package version: \cs{1.2.0}}}
 
 \thispagestyle{empty}
 \maketitle