Question: Formal class VRanges versus Large VRanges
0
gravatar for guillaume.dachy
14 months ago by
Brussels
guillaume.dachy0 wrote:

Hi everyone, 

I am using the SomaticSignatures package with my "usual" script but I get today an error thath I don't manage to fix. 

By importing VCF files with the readVcfAsVRanges function, I get two different objects of different classes incompatible with each other (I can't build a vector to go futher in the analysis). 

VCF are output of Mutect2 pipeline. 

Here is an example of the code I use: 

vr_HNC7 = readVcfAsVRanges("C:/path/to/HNC7.vcf", "GenomeA")
mcols(vr_HNC7)$sample = "HNC7"

vr_HNC9 = readVcfAsVRanges("C:/path/to/HNC9.vcf", "GenomeA")
mcols(vr_HNC9)$sample = "HNC9"

This give me 2 different objects : a "Formal class VRanges" for HNC7 and a "Large VRanges" for HNC9. The only difference is the number of variant (and so the dimensions of the matrix), respectively 50x114 and 167x114. 

When I try to make a vector :

vr_HNCtot = c(vr_HNC2, vr_HNC4, vr_HNC7, vr_HNC9, vr_HNC10, vr_HNC12)
Error in rbind(...) : 
  number of columns of matrices must match (see arg 5)

Is there a way to get the same kind of object to be able to merge them in a vector and to make the SomaticSignatures analysis ?? 

Thanks a lot !!

Cheers

Guillaume

ADD COMMENTlink modified 14 months ago • written 14 months ago by guillaume.dachy0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 308 users visited in the last hour