Question: Extracting CNV data from CNVDetectionResult
0
gravatar for abdul.elkadri
4.4 years ago by
Canada
abdul.elkadri0 wrote:

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!

cn.mops • 1.3k views
ADD COMMENTlink modified 4.0 years ago by Günter Klambauer540 • written 4.4 years ago by abdul.elkadri0
Answer: Extracting CNV data from CNVDetectionResult
1
gravatar for Günter Klambauer
4.4 years ago by
Austria
Günter Klambauer540 wrote:

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

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Günter Klambauer540

Yes it does! We were able to extract the table in a useable format. 

 

Thanks for your help!

ADD REPLYlink written 4.4 years ago by abdul.elkadri0

which dataframe is  used to generate the segplot?

ADD REPLYlink written 3.1 years ago by tangming2005150

Works like a charm! Thank you :)

ADD REPLYlink written 2.8 years ago by anilkanthi0
Answer: Extracting CNV data from CNVDetectionResult
0
gravatar for peng.zhang
4.1 years ago by
peng.zhang0
United States
peng.zhang0 wrote:

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

ADD COMMENTlink written 4.1 years ago by peng.zhang0
Answer: Extracting CNV data from CNVDetectionResult
0
gravatar for legatiandrea
4.0 years ago by
Italy
legatiandrea0 wrote:

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

ADD COMMENTlink written 4.0 years ago by legatiandrea0
Answer: Extracting CNV data from CNVDetectionResult
0
gravatar for Günter Klambauer
4.0 years ago by
Austria
Günter Klambauer540 wrote:

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

Günter

ADD COMMENTlink written 4.0 years ago by Günter Klambauer540
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