Formal class VRanges versus Large VRanges
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Last seen 3.8 years ago

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 !!



somaticsignatures vranges readvcfasvranges • 716 views

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