Error with cn.MOPS run on exomeseq data

Question

[vakul.mohanty]

Hello,

I'm having trouble with cn.MOPS. I run the following piece of code and receive an error

library(cn.mops)
bam = list.files(path = "/home/trantor/mounts/komurov_lab/SKCM_WES",pattern=".bam$",full.names=TRUE)
seg = read.table(file = "/home/trantor/mounts/komurov_lab/Ensemble_exon", sep="\t",as.is =TRUE)
gr = GRanges(seg[,1],IRanges(seg[,2],seg[,3]))
seqlevels(gr) = gsub("chr","",seqlevels(gr))
gr = disjoin(gr)
#specifing the chromosome to run the analysis on
gr = gr[seqnames(gr) == "1"]
count = getSegmentReadCountsFromBAM(bam, GR=gr, mode="paired")
res = exomecn.mops(count)

Error:

Normalizing...
Error in normalizeChromosomes(X, chr = chr, normType = normType, qu = normQu) :
  Some normalization factors are zero! Remove samples or chromosomes for which the average read count is zero, e.g. chromosome Y

My GRanges object is limited to chromosome 1 and the count object shows counts in every sample so I'm not quiet sure how the normalization factor is zero.

I will be grateful for help with this.

Thanking You,

Vakul