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XCMS / Re: Add spectra of xcmsRaw objects together & write to cdf
OK, figured out how to do it, maybe not the most elegant solution, but it seems to work. Currently, I assume that your different files are already reasonably well aligned.
Code: [Select]
######### function to sum the spectra of two xcmsRaw objects together and return it as a new xcmsRaw object
addspectra = function(object1,object2,profst=1) {
mzminobj1=min(object1@mzrange)
mzmaxobj1=max(object1@mzrange)
mzminobj2=min(object2@mzrange)
mzmaxobj2=max(object2@mzrange)
mzmin=min(mzminobj1,mzminobj2)
mzmax=max(mzmaxobj1,mzmaxobj2)
if (mzmin<mzminobj1) {object1@env$profile=rbind(matrix(0,nrow=round((mzminobj1-mzmin)/profst),ncol=ncol(object1@env$profile)),object1@env$profile)}
if (mzmin<mzminobj2) {object2@env$profile=rbind(matrix(0,nrow=round((mzminobj2-mzmin)/profst),ncol=ncol(object2@env$profile)),object2@env$profile)}
if (mzmax>mzmaxobj1) {object1@env$profile=rbind(object1@env$profile,matrix(0,nrow=round((mzmax-mzmaxobj1)/profst),ncol=ncol(object1@env$profile)))}
if (mzmax>mzmaxobj2) {object2@env$profile=rbind(object2@env$profile,matrix(0,nrow=round((mzmax-mzmaxobj2)/profst),ncol=ncol(object2@env$profile)))}
object1@mzrange=c(mzmin,mzmax)
object2@mzrange=c(mzmin,mzmax)
object3=object1
object3@env$profile=object1@env$profile+object2@env$profile # matrix with scans in columns and rows representing equally spaced m/z values
object3@tic=object1@tic+object2@tic
nscans=ncol(object1@env$profile)
mznew=c()
intensitynew=c()
scanindexnew=c()
mzall=seq(mzmin,mzmax,by=profst)
x=object3@env$profile
intensitynew=lapply(seq_len(ncol(x)), function(i) {res=x[,i];res[res!=0]})
mznew=lapply(seq_len(ncol(x)), function(i) {res=x[,i];mzall[res!=0]})
scanindexnew=sapply(seq_len(length(mznew)), function(i) {length(mznew[[i]])})
scanindexnew=c(0,scanindexnew)[1:length(scanindexnew)]
scanindexnew=sapply(seq_len(length(scanindexnew)), function(i) {sum(scanindexnew[1:i])})
object3@env$mz=unlist(mznew)
object3@env$intensity=unlist(intensitynew)
object3@scanindex=as.integer(scanindexnew)
return(object3)
}
######### function to sum the spectra of several cdf files and write it back as a cdf file
addspectracdffiles = function(files,profst=1,outfile="summedspectra.cdf") {
obj=xcmsRaw(files[1],profstep=profst,profmethod="bin")
nfiles=length(files)
if (nfiles>1) {
for (i in 2:length(files)) {
obj2=xcmsRaw(files[i],profstep=profst,profmethod="bin")
obj=addspectra(obj,obj2,profst=profst)
print(paste("Added spectrum of file",files[i]))
}}
write.cdf(obj,file=outfile)
return(obj)
}