Dear all,

When I use makeVRangesFromGRanges (R package VariantAnnotation), I got the following error,

Error in as(mcols(gr)[, i], type[i]) : no method or default for coercing "factor" to "NA"

My operations shown below

> library(SomaticSignatures)
> data(ov_tcga, package = "SomaticCancerAlterations")
> ov_tcga_2_vr <- makeVRangesFromGRanges(ov_tcga, ref.field="Reference_Allele", alt.field = "Tumor_Seq_Allele2")

Error in as(mcols(gr)[, i], type[i]) :
no method or default for coercing "factor" to "NA"

Can anybody help me to solve this problem? Thank.

I think this is a bug in VariantAnnotation 1.18.1 / 1.19.5. A work-around is to make the order of the columns of the GRanges match the order in the argument list

idx = match(c("Reference_Allele", "Tumor_Seq_Allele2"), names(mcols(ov_tcga)))
mcols(ov_tcga) = cbind(mcols(ov_tcga)[idx], mcols(ov_tcga)[-idx])