Mercurial > repos > lecorguille > xcms_xcmsset

comparison xcms_xcmsSet.r @ 36:d39b9aff9cf7 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
author lecorguille
date Thu, 05 Apr 2018 18:05:45 -0400
parents 7f636ad1162b
children 9ada611dd63f
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35:7f636ad1162b 36:d39b9aff9cf7
99 xdata@processingData@files <- sub(paste(getwd(), "/", sep="") , "", xdata@processingData@files) 99 xdata@processingData@files <- sub(paste(getwd(), "/", sep="") , "", xdata@processingData@files)
100 100
101 # Create a sampleMetada file 101 # Create a sampleMetada file
102 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv") 102 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
103 103
104 cat("\t\t\tCompute and Store TIC and BPI\n")
105 chromTIC = chromatogram(xdata, aggregationFun = "sum")
106 chromBPI = chromatogram(xdata, aggregationFun = "max")
107
104 cat("\n\n") 108 cat("\n\n")
105 109
106 # ----- EXPORT ----- 110 # ----- EXPORT -----
107 111
108 cat("\tXCMSnExp OBJECT INFO\n") 112 cat("\tXCMSnExp OBJECT INFO\n")
114 xset <- getxcmsSetObject(xdata) 118 xset <- getxcmsSetObject(xdata)
115 print(xset) 119 print(xset)
116 cat("\n\n") 120 cat("\n\n")
117 121
118 #saving R data in .Rdata file to save the variables used in the present tool 122 #saving R data in .Rdata file to save the variables used in the present tool
119 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") 123 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList", "chromTIC", "chromBPI")
120 save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData") 124 save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData")
121 125
122 126
123 cat("\tDONE\n") 127 cat("\tDONE\n")