Hi,

I am trying to upload TCGA level1 methylation data from 27k. I've tried to
follow instructions for Glioblastoma example as well but I had a problem
with installation of TCGAGBM package so I was not able see the format of
the files of the example data. I've tried different versions of the
following script but at some point (I think from the point I indicated) it
does not work properly. I would be very grateful for help.

Best wishes,
Magdalena


homedir="D:/TCGA Methylation Analysis/DATA/KIRC/LEVEL
1/Pairs_HumanMethylation27"
dirs=list.files(homedir)
batchNames=gsub("jhu-usc.edu_KIRC.HumanMethylation27.","",dirs)
tmp=sapply(strsplit(batchNames,"\\."),function(x) as.numeric(x[1:2]))

files=vector("list",length(dirs))
ngenes=27578
for(i in seq(along=dirs)){
  tmpPath=file.path(homedir,dirs[i])
  fns=list.files(tmpPath)
  files[[i]]=fns[grep("lvl-1",fns)]
}

nfiles=sapply(files,length)
starts=c(0,cumsum(nfiles[-length(nfiles)]))
*
### FROM HERE SOMETHING DOESN'T WORK*
# b = tmp$Methylated_Signal_Intensity..M./
   (tmp$Methylated_Signal_Intensity..M.
    + tmp$Un.Methylated_Signal_Intensity..U.+100)
# betas=matrix(b,nrow=ngenes,ncol=sum(nfiles))
betas=matrix(NA,nrow=ngenes,ncol=sum(nfiles))
cnames=vector("character",sum(nfiles))
batch=factor(rep(seq(along=files),nfiles))
for(i in seq(along=dirs)){
  cat(i)
  tmpPath=file.path(homedir,dirs[i])
  fns=files[[i]]
  for(j in seq(along=fns)){
    cat(".")

    ###Get the sample name
tmp=strsplit(readLines(file.path(tmpPath,fns[j]),n=1),"\t")
cnames[ j+starts[i] ]=tmp[[1]][2]

    ##Get the Beta values
tmp=read.delim(file.path(tmpPath,fns[j]),skip=1,check.names=FALSE,as.is
=TRUE)
b=
    betaIndex=grep("[bB]eta",names(tmp)) ##the column name change!!
betas[,j+starts[i]]=tmp[,betaIndex]

    ###Check "gene" names in same order
if(i==1 & j==1) gnames=tmp[,"CompositeElement REF"] else
if(!identical(gnames,tmp[,"CompositeElement REF"])) stop("Genes not in
order")
  }
cat("\n")
}
colnames(betas)=cnames
rownames(betas)=gnames

save(betas,batch,batchNames,file="betas.rda")

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