comparison xcms_xcmsSet.r @ 34:efd23113d5f4 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309

33:c363b9f1caef

xdata@processingData@files <- sub(paste(getwd(), "/", sep="") , "", xdata@processingData@files)

# Create a sampleMetada file
sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")

# Get the legacy xcmsSet object
xset <- getxcmsSetObject(xdata)

cat("\n\n")


# -- TIC --
cat("\t\tGET TIC GRAPH\n")
#@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method
getTICs(xcmsSet=xset, rt="raw", pdfname="TICs.pdf")
getBPCs(xcmsSet=xset, rt="raw", pdfname="BICs.pdf")

cat("\n\n")

# ----- EXPORT -----

cat("\tXCMSnExp OBJECT INFO\n")
print(xdata)
cat("\n\n")

cat("\txcmsSet OBJECT INFO\n")
print(xset)
cat("\n\n")

#saving R data in .Rdata file to save the variables used in the present tool
objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")

34:efd23113d5f4

xdata@processingData@files <- sub(paste(getwd(), "/", sep="") , "", xdata@processingData@files)

# Create a sampleMetada file
sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")

cat("\n\n")

# ----- EXPORT -----

cat("\tXCMSnExp OBJECT INFO\n")
print(xdata)
cat("\n\n")

cat("\txcmsSet OBJECT INFO\n")
# Get the legacy xcmsSet object
xset <- getxcmsSetObject(xdata)
print(xset)
cat("\n\n")

#saving R data in .Rdata file to save the variables used in the present tool
objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")