Question: cn.MOPS - reporting log normalized read counts as table
0
gravatar for falk.zakrzewski
24 months ago by
falk.zakrzewski0 wrote:

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

 

ADD COMMENTlink modified 24 months ago by Günter Klambauer540 • written 24 months ago by falk.zakrzewski0
Answer: cn.MOPS - reporting log normalized read counts as table
1
gravatar for Günter Klambauer
24 months ago by
Austria
Günter Klambauer540 wrote:

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

ADD COMMENTlink written 24 months ago by Günter Klambauer540

Many thanks! It works.

ADD REPLYlink written 24 months ago by falk.zakrzewski0
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