I am using the very interesting SomaticSignatures package, and I have an Error now for which I didn't manage to find an answer on this support site.
I managed to concatenate some VRanges objects to one, and so all the functions are working wonderfully to get some signatures, but for others objects I do not manage to build the vector and the results are two different kind of Errors (depending on the VRanges objects I try to concatenate).
Here is the code :
1) "vr_caf34" is one of the VCF file transformed in VRange, so you see the method I used :
> vr_caf34 = readVcfAsVRanges("C:/path/to/vcf_CDS/CAFSARC34.pPDGFRBCDS.torrent.snpEff.vcf", "GenomeA") > mcols(vr_caf34)$sample = "caf34" > vr_CDS = c(vr_caf32, vr_caf33, vr_caf34, vr_caf40, vr_caf41, vr_caf46, vr_caf50, vr_caf60, vr_caf62, vr_caf63, vr_caf64) > vr_CDS VRanges object with 1705 ranges and 63 metadata columns: Error: subscript is a NSBS object that is incompatible with the current subsetting operation
2) Trying to combine other VRanges objects (from other VCF files), I get :
> vr_caf2 = readVcfAsVRanges("C:/path/to/vcf_PAPBKIT/CAFSARC-2.pPAPBKIT.torrent.snpEff.vcf", "GenomeA") > mcols(vr_caf2)$sample = "caf2" > vr_PAPBKIT = c(vr_caf2, vr_caf7, vr_caf9, vr_caf10, vr_caf11, vr_caf15, vr_caf16, vr_caf18) Error in combine_CompressedList_objects(class(x), objects, use.names = FALSE, : the objects to combine must be CompressedList objects (or NULLs)
I tried several times today, but I can't find a solution. My R version is uptodate and so are the packages I am using (I think...).
Thank you so much for your help !