Question: Error with plotting with target sequencing data
0
gravatar for jinxinhao1988
17 months ago by
jinxinhao19880 wrote:

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,

 

 

cn.mops • 291 views
ADD COMMENTlink modified 17 months ago by Günter Klambauer540 • written 17 months ago by jinxinhao19880
Answer: Error with plotting with target sequencing data
0
gravatar for Günter Klambauer
17 months ago by
Austria
Günter Klambauer540 wrote:

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

ADD COMMENTlink written 17 months ago by Günter Klambauer540
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