Mercurial > repos > lecorguille > xcms_xcmsset

comparison xcms_xcmsSet.r @ 31:eb15a3841da4 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
author workflow4metabolomics
date Tue, 28 Apr 2020 09:35:10 -0400
parents 14b1c52fae62
children b02d1992a43a
comparison
equal deleted inserted replaced
30:14b1c52fae62 31:eb15a3841da4
38 38
39 #saving the specific parameters 39 #saving the specific parameters
40 if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum 40 if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum
41 if (!is.null(args$filterRt)) filterRtParam <- args$filterRt 41 if (!is.null(args$filterRt)) filterRtParam <- args$filterRt
42 if (!is.null(args$filterMz)) filterMzParam <- args$filterMz 42 if (!is.null(args$filterMz)) filterMzParam <- args$filterMz
43 if (!is.null(args$peaklist)) peaklistParam <- args$peaklist
43 44
44 method <- args$method 45 method <- args$method
45 46
46 if (!is.null(args$roiList)){ 47 if (!is.null(args$roiList)){
47 cat("\t\troiList provided\n") 48 cat("\t\troiList provided\n")
98 99
99 #cat("\t\t\tCompute and Store TIC and BPI\n") 100 #cat("\t\t\tCompute and Store TIC and BPI\n")
100 #chromTIC = chromatogram(xdata, aggregationFun = "sum") 101 #chromTIC = chromatogram(xdata, aggregationFun = "sum")
101 #chromBPI = chromatogram(xdata, aggregationFun = "max") 102 #chromBPI = chromatogram(xdata, aggregationFun = "max")
102 103
104 # Create a chromPeaks table if required
105 if (exists("peaklistParam")) {
106 if(peaklistParam){
107 cat("\nCreating the chromatographic peaks' table...\n")
108 write.table(chromPeaks(xdata), file="chromPeak_table.tsv",sep="\t",quote=F,row.names=F)
109 }
110 }
111
103 cat("\n\n") 112 cat("\n\n")
104 113
105 # ----- EXPORT ----- 114 # ----- EXPORT -----
106 115
107 cat("\tXCMSnExp OBJECT INFO\n") 116 cat("\tXCMSnExp OBJECT INFO\n")