Nothing
readMethylome <-
function(FileName, seqLengths, format="text"){
message("reading methylome data")
if(format=="GRanges"){
meth <- readRDS(FileName)
}
else if(format=="text"){
dat <- scan(FileName, what=list(chr=character(0), pos=integer(0), T=double(0), M=double(0)), sep="\t")
meth <- GRanges(seqnames=dat$chr, ranges=IRanges(start=dat$pos, width=1), strand='*', T=dat$T, M=dat$M, seqlengths=seqLengths)
}
else{
stop("unknown format")
}
mean.cov=mean(values(meth)[, 1])
if(mean.cov < 10)
warning(sprintf("We do not recommend the use of MethylSeekR\nfor methylomes with mean coverage < 10X\n(mean coverage of CpGs with at least one read: %.1f)", mean.cov))
# order by chromosome and CpG position
meth <- meth[order(as.vector(seqnames(meth)), start(meth))]
meth
}
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