Question: varscan2: merge the CNA segments using
gravatar for Chirag Nepal
4.3 years ago by
Chirag Nepal2.2k
Chirag Nepal2.2k wrote:

Hi There,

I did copynumber call and performed segmentation using DNAcopy.


cnP1 = read.table ("copyNumber_varscanIdhP1.copynumber", header=TRUE)
CNA.object <- CNA( genomdat = cnP1[,7], chrom = cnP1[,1], maploc = cnP1 [,2], data.type = 'logratio')

CNA.object.smoothed     <- smooth.CNA(CNA.object)
CNA.object.smoothed.seg <- segment(CNA.object.smoothed, verbose=0, min.width=2)
segmented = CNA.object.smoothed.seg$output
write.table (segmented[,2:6], file="cbsP1", row.names=F, col.names=F, quote=F, sep="\t")


Now, i want to merge these output segments:

USAGE: [segments] OPTIONS
        segments - A segments file with p-values from the DNAcopy library. This should be tab- or space-delimited
        with a header and the following columns: ID, chrom, loc.start, loc.end, num.mark, seg.mean, bstat, pval, lcl, ucl.


WHAT is the input file here ?

Is the input to the script is output from DNAcopy output.

But the columns are different:

head cbs_P1
chr1    567331    569882    6    -2.3721
chr1    761847    905536    162    -0.1232
chr1    905636    3549990    2846    -0.0335


Can you please suggest me to make the input file in compatible format.

thanks !

Edit:  This is how you could get input file (output from DNACopy) to

seg.pvalue <- segments.p(CNA.object.smoothed.seg, ngrid=100, tol=1e-6, alpha=0.05, search.range=100, nperm=1000)
write.table (seg.pvalue, file="blah", row.names=F, col.names=F, quote=F, sep="\t")







cnv varscan • 2.3k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Chirag Nepal2.2k
gravatar for poisonAlien
4.3 years ago by
poisonAlien2.8k wrote:

Its the output from segments.p function from DNACopy.

ADD COMMENTlink written 4.3 years ago by poisonAlien2.8k
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