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Topic: Peak Picked TIC (Read 2545 times) previous topic - next topic

  • hpbenton
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Peak Picked TIC
You want to create a TIC of the peaks that were picked. Either that or you don't have the original files to reload.
The code below allows you to take an xcmsSet object or xsAnnotate object and create the peak picked EIC.

Code: [Select]
xcmsSet.TIC<-function(object,...){
if(class(object) == "xsAnnotate"){
object<-object@xcmsSet
}
Intensity<-rowMeans(groupval(object, "medret", "maxo"))
rt<-object@groups[,"rtmed"]
idx<-order(rt)

plot(x=rt[idx], y=Intensity[idx], type="b",
ylab="Intensity", xlab="Retention time (sec)",
main="Peak picked TIC", ...)
}
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page