We have been using cn.mops to run CNV analysis on a whole genome sequencing dataset. Is it possible to extract the data from the CNVDetectionResult object which is used to plot the graph seen through segplot?

We are unsure which CNVDetectionResult Method is appropriate to extract the true copy number variant we are looking for. We are looking to create a dataset which will be used to scan for genomic copy number variants and includes predicted copy number and genomic position. 

Thanks for the replies in advance!

Hello Abdul,

I think the question is about extracting and exporting the result of cn.MOPS. Let us assume you have the result of cn.MOPS as the following:

library(cn.mops); data(cn.mops)

result <- calcIntegerCopyNumbers(cn.mops(XRanges))

You can extract the segmentation, the CNVs and the CNV regions with the following:

segm <- as.data.frame(segmentation(result))

CNVs <- as.data.frame(cnvs(result))

CNVRegions <- as.data.frame(cnvr(result))

You can export the result with "write.csv" for Excel, LibreOffice Calc etc:

write.csv(segm,file="segmentation.csv")

write.csv(CNVs,file="cnvs.csv")

write.csv(CNVRegions,file="cnvr.csv")

This files will include the genomic position, copy number and other information. Does this answer your question?

Regards,

Günter

This is very useful for me, it would be great if it can be incorporated in the cn.mops manual.

Usefeul also for me, I quote the comment before, it would be great if it can be incorporated in the manual!

Added to the manual - thanks for the comments!
Regards,

Günter