cn.MOPS - reporting log normalized read counts as table
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@falkzakrzewski-13567
Last seen 5.7 years ago

Dear developer team,

 

many thanks for the great tool cn.MOPS which I am running in R. It is very helpful for our analysis.  

 

May I ask you whether it is possible to report also the log normalized read counts (used for the seqplot function) as .csv table similar to the functions:

 

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

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

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

 

Many thanks for your help and

Best regards

 

cn.mops log normalized counts table • 1.8k views
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@gunter-klambauer-5426
Last seen 3.8 years ago
Austria

There is a hidden function called ".makeLogRatios" that you can apply to the cn.mops result object:

library(cn.mops)
data(cn.mops)
res <- cn.mops(XRanges)
logRatios <- cn.mops:::.makeLogRatios(res)
as.data.frame(logRatios)

 

Regards,

Günter

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Many thanks! It works.

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