I am using the Bioconductor package SomaticSignatures. Since I am very new to NSG anaysis, I tried to reproduce the example used in the Read.me of the package. However, I run into some problems when extracting the sequence context (Section 4.2). I got the following error message.
Error in mutationContext(sca_vr, BSgenome.Hsapiens.1000genomes.hs37d5) : Only SNV substitutions are currently supported.
I tried to work around this by subsetting the VRanges object using this:
SNV=isSNV(sca_vr) sca_vrSNV <- sca_vr[SNV]
sca_motif=mutationContext(sca_vrSNV,BSgenome.Hsapiens.1000genomes.hs37d5) Error in mutationContext(sca_vrSNV, BSgenome.Hsapiens.1000genomes.hs37d5) : Only SNV substitutions are currently supported
... still gave me the same error message.
I also verified that the
isSNV(sca_vrSNV) still return TRUE only.
Has anyone had a similar problem? Or do you see some obvious mistake?
Thanks for the help!