Hi everyone,

I get this error message when i try to set a genotype to a VCF object:

> geno(object@VCF)

List of length 0

> SimpleList(GT=GenotypeAsMatrix,GL=GenotypeLikAsMatrix)

List of length 2

names(2): GT GL

> geno(object@VCF) <- SimpleList(GT=GenotypeAsMatrix,GL=GenotypeLikAsMatrix)

Error in `assays<-`(`*tmp*`, value = <S4 object of class "SimpleList">) : 

  current and replacement dimnames() differ

> traceback()

5: stop("current and replacement dimnames() differ")

4: `assays<-`(`*tmp*`, value = <S4 object of class "SimpleList">)

3: `assays<-`(`*tmp*`, value = <S4 object of class "SimpleList">)

2: `geno<-`(`*tmp*`, value = <S4 object of class "SimpleList">)

1: `geno<-`(`*tmp*`, value = <S4 object of class "SimpleList">)

> sessionInfo()

R version 3.2.5 (2016-04-14)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu precise (12.04.5 LTS)

Does somebody have an idea ?

Thanks

The dimnames in the SimpleList matrices should match the dimnames of the VCF object.  For example, from the help page ?geno 

library(VariantAnnotation)
fl <- system.file("extdata", "ex2.vcf", 
                          package="VariantAnnotation")
vcf <- readVcf(fl, genome="hg19")
dimnames(vcf)
dimnames(geno(vcf)[["GT"]]) = list(LETTERS[1:5], letters[1:3])

This generates the error you have experienced because it is trying to rename dimnames(geno(vcf)[["GT"]]) to something other than the dimnames(vcf)