I want to create a mutation count matrix from an expanded vcf file. I tried the genCountMatrixFromVcf() from signeR package. I am getting the following error, and I can't find any other function to create mutation count matrix.

mutcounts <- genCountMatrixFromVcf(BSgenome.Hsapiens.UCSC.hg19, onlyvariants) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘alt<-’ for signature ‘"ExpandedVCF", "DNAStringSetList"’

Thanks in advance, Nikita Naik