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)
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.