Dear all,

I use cn.mops to run CNV test in one sample without control. My data is Targeted sequencing data. It runs good until the plotting procedure.

I use the command line as follows:

> library(cn.mops)
> BAMFiles <- list.files(pattern=".bam$")
> segments <- read.table("targetRegions.bed",sep="\t",as.is=TRUE)
> gr <- GRanges(segments[,1],IRanges(segments[,2],segments[,3]))
> X <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr,mode="paired",)
> resCNMOPS <- exomecn.mops(X)
> resCNMOPS <- calcIntegerCopyNumbers(resCNMOPS)
> plot(resCNMOPS,which=5)

and I got the errors:

dev.new(): using pdf(file="Rplots1.pdf")
Error in .local(x, ...) : Selected unknown CNVR for plotting.

It seems that there is some problem with the CNV region.

Then I change the code into: 

> plot(resCNMOPS,which=1)

This time there is no error. BUT there is no output file either.

I checked my resCNMOPS, It's like this:

I think that the results seems fine. So I wonder what's wrong with the plotting. Is it because my target regions are not consecutive?

Thank you for your time.

Best regards,

Hello,

Thanks for using cn.mops. This error could also be related to the graphics devices. Could you please check if the error persist when you use other graphics devices (e.g. "pdf("tmp.pdf"); plot(resCNMOPS,which=5); dev.off()". If the error persists, please run "traceback()" directly after the error occurs. If nothing helps, please send me the "resCNMOPS"-object via email and I will see if I can find the problem.

Regards,
Günter