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Hello!
I am currently using cn.mops on several control/tumor samples (WGS).
I used the pipeline for bulk comparison as described by the author:
bam <- list.files(path, pattern=".bam$") bamDataRanges <- getReadCountsFromBAM(bam, mode="paired", parallel=2) cn1 <- cn.mops(bamDataRanges) cn2 <- calcIntegerCopyNumbers(cn1) cnvs(cn2) cnvr(cn2)
getting several CNV with the expected format.
Then I used it for tumor (n=5) vs control (n=5)
resRef <- referencecn.mops(cases=cases, controls=controls, classes=c("CN0", "CN1", "CN2", "CN3", "CN4", "CN5", "CN6", "CN7", "CN8", "CN16", "CN32", "CN64", "CN128"), I=c(0.025, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 8, 16, 32, 64))
My issue is that after calling I get a table that display only NA values in the "CN" column (with cnvr/cnvs):
cnvs(resRef) seqnames ranges strand | sampleName median mean CN <Rle> <IRanges> <Rle> | <factor> <numeric> <numeric> <logical> [1] 1 [12667001, 12671000] * | Tumor1.bam -5.3219281 -5.3219 <NA>
Can someone explain me the reason?
Thanks in advance!
Hi!
As advised I upgraded bioconductor/cn.mops to the lastest version. This seem to have solved the issue.
Thanks for your quick answer.