Mercurial > repos > pieterlukasse > prims_metabolomics

comparison xcms_differential_analysis.r @ 2:627ddbd15823

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
using tool_dependencies file
author pieter.lukasse@wur.nl
date Fri, 24 Oct 2014 16:44:03 +0200
parents 071a185c2ced
children ddef5534c294
comparison
equal deleted inserted replaced
1:071a185c2ced 2:627ddbd15823
28 sink(msg, type="message") 28 sink(msg, type="message")
29 sink(msg, type="output") 29 sink(msg, type="output")
30 30
31 tryCatch( 31 tryCatch(
32 { 32 {
33 library(metaMS)
33 library(xcms) 34 library(xcms)
34 #library("R2HTML") 35 #library("R2HTML")
35 36
36 ## load the constructed DB : 37 ## load the constructed DB :
37 xcmsSet <- readRDS(args.xsetData) 38 xcmsSet <- readRDS(args.xsetData)
45 46
46 message("\nGenerating report.........") 47 message("\nGenerating report.........")
47 # report 48 # report
48 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE) 49 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE)
49 # setwd(file.path(args.htmlReportFile.files_path)) 50 # setwd(file.path(args.htmlReportFile.files_path))
51 file.rename("fig_eic", paste(args.htmlReportFile.files_path, "/fig_eic"))
52
50 53
51 cat("<html><body><h1>Differential analysis report</h1>", file= args.htmlReportFile) 54 cat("<html><body><h1>Differential analysis report</h1>", file= args.htmlReportFile)
52 #HTML(reporttab[1:args.topcount,], file= args.htmlReportFile) 55 #HTML(reporttab[1:args.topcount,], file= args.htmlReportFile)
53 figuresPath <- paste(args.htmlReportFile.files_path, "_eic", sep="") 56 figuresPath <- paste(args.htmlReportFile.files_path, "_eic", sep="")
54 message(figuresPath) 57 message(figuresPath)