Question: Formal class VRanges versus Large VRanges
0
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