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!

Hello Radek,

Thanks for using cn.mops!

This functionality should actually work. The return object should 
contain the integer copy numbers of the cases. Could you please upgrade 
to the most recent version of R / Bioconductor / cn.mops and check if 
the problem persists? If yes, could you give me a minimal example that 
reproduces the error?

Regards,
Günter