Mercurial > repos > pieterlukasse > prims_metabolomics

comparison xcms_differential_analysis.r @ 49:f772a5caa86a

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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
comparison
equal deleted inserted replaced
48:26b93438f30e 49:f772a5caa86a
12 12
13 args.topcount <- strtoi(args[4]) 13 args.topcount <- strtoi(args[4])
14 #cat(paste("args.topcount <- ", args[4], "\n", sep="")) 14 #cat(paste("args.topcount <- ", args[4], "\n", sep=""))
15 15
16 args.outTable <- args[5] 16 args.outTable <- args[5]
17 args.outLogFile <- args[6]
18 #cat(paste("args.outLogFile <- \"", args[6], "\"\n", sep=""))
19 17
20 ## report files 18 ## report files
21 args.htmlReportFile <- args[7] 19 args.htmlReportFile <- args[6]
22 args.htmlReportFile.files_path <- args[8] 20 args.htmlReportFile.files_path <- args[7]
23 #cat(paste("args.htmlReportFile <- \"", args[7], "\"\n", sep="")) 21 #cat(paste("args.htmlReportFile <- \"", args[6], "\"\n", sep=""))
24 #cat(paste("args.htmlReportFile.files_path <- \"", args[8], "\"\n", sep="")) 22 #cat(paste("args.htmlReportFile.files_path <- \"", args[7], "\"\n", sep=""))
25 23
26 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888 24
27 msg <- file(args.outLogFile, open="wt") 25 if (length(args) == 8)
28 sink(msg, type="message") 26 {
29 sink(msg, type="output") 27 args.outLogFile <- args[8]
28 # suppress messages:
29 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
30 msg <- file(args.outLogFile, open="wt")
31 sink(msg, type="message")
32 sink(msg, type="output")
33 }
30 34
31 tryCatch( 35 tryCatch(
32 { 36 {
33 library(metaMS) 37 library(metaMS)
34 library(xcms) 38 library(xcms)
35 #library("R2HTML") 39 #library("R2HTML")
36 40
37 ## load the constructed DB : 41 # load the xset data :
38 xcmsSet <- readRDS(args.xsetData) 42 xsetData <- readRDS(args.xsetData)
43 # if here to support both scenarios:
44 if ("xcmsSet" %in% slotNames(xsetData) )
45 {
46 xsetData <- xsetData@xcmsSet
47 }
48
39 49
40 # info: levels(xcmsSet@phenoData$class) also gives access to the class names 50 # info: levels(xcmsSet@phenoData$class) also gives access to the class names
41 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE) 51 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
42 reporttab <- diffreport(xcmsSet, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640) 52 reporttab <- diffreport(xsetData, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640)
43 53
44 # write out tsv table: 54 # write out tsv table:
45 write.table(reporttab, args.outTable, sep="\t", row.names=FALSE) 55 write.table(reporttab, args.outTable, sep="\t", row.names=FALSE)
46 56
47 message("\nGenerating report.........") 57 message("\nGenerating report.........")