Mercurial > repos > pieterlukasse > prims_metabolomics
diff xcms_differential_analysis.r @ 49:f772a5caa86a
Added more options and better documentation.
Added MsClust support for parsing XCMS alignment results.
Improved output reports for XCMS wrappers.
New tools.
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 10 Dec 2014 22:03:27 +0100 |
| parents | e67149fbff20 |
| children | 10f3cb998c4e |
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--- a/xcms_differential_analysis.r Wed Nov 19 15:11:45 2014 +0100 +++ b/xcms_differential_analysis.r Wed Dec 10 22:03:27 2014 +0100 @@ -14,19 +14,23 @@ #cat(paste("args.topcount <- ", args[4], "\n", sep="")) args.outTable <- args[5] -args.outLogFile <- args[6] -#cat(paste("args.outLogFile <- \"", args[6], "\"\n", sep="")) ## report files -args.htmlReportFile <- args[7] -args.htmlReportFile.files_path <- args[8] -#cat(paste("args.htmlReportFile <- \"", args[7], "\"\n", sep="")) -#cat(paste("args.htmlReportFile.files_path <- \"", args[8], "\"\n", sep="")) +args.htmlReportFile <- args[6] +args.htmlReportFile.files_path <- args[7] +#cat(paste("args.htmlReportFile <- \"", args[6], "\"\n", sep="")) +#cat(paste("args.htmlReportFile.files_path <- \"", args[7], "\"\n", sep="")) + -# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888 -msg <- file(args.outLogFile, open="wt") -sink(msg, type="message") -sink(msg, type="output") +if (length(args) == 8) +{ + args.outLogFile <- args[8] + # suppress messages: + # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888 + msg <- file(args.outLogFile, open="wt") + sink(msg, type="message") + sink(msg, type="output") +} tryCatch( { @@ -34,12 +38,18 @@ library(xcms) #library("R2HTML") - ## load the constructed DB : - xcmsSet <- readRDS(args.xsetData) + # load the xset data : + xsetData <- readRDS(args.xsetData) + # if here to support both scenarios: + if ("xcmsSet" %in% slotNames(xsetData) ) + { + xsetData <- xsetData@xcmsSet + } + # info: levels(xcmsSet@phenoData$class) also gives access to the class names - dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE) - reporttab <- diffreport(xcmsSet, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640) + dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE) + reporttab <- diffreport(xsetData, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640) # write out tsv table: write.table(reporttab, args.outTable, sep="\t", row.names=FALSE)