GENESIS does support imputed dosages, but if you are starting with VCF files there is an extra conversion step involved to get this to work.
For imputed dosages in VCF format, use the SeqArray package:
seqVCF2GDSto convert your VCF file to a SeqArray GDS file
seqGDS2SNPwith the argument
dosage=TRUEto convert that file to a GDS format supporting dosage in the "genotype" node
For imputed dosages in other formats (IMPUTE2, BEAGLE, MACH), use the GWASTools package:
imputedDosageFileto convert directly to a GDS file with dosage in the "genotype" node
Finally, use the GWASTools package to create a
GenotypeData object for use in GENESIS. See the vignette for an example of running association tests with
GenotypeData objects: https://bioconductor.org/packages/devel/bioc/vignettes/GENESIS/inst/doc/assoc_test.html
In the next development cycle, we plan to add support for reading dosages directly from SeqArray GDS files.
As of version 2.13.2, GENESIS supports the use of imputed dosages directly from SeqArray GDS files in association testing. Convert a VCF with imputed dosages preserving the dosage field:
seqVCF2GDS(vcffile, gdsfile, fmt.import="DS")
assocTestAggregate with option
SeqVarTools version 1.21.1 or later is required to use this feature.