seqAsVCF {SeqArray} | R Documentation |
Create a VCF-class object
seqAsVCF(x, chr.prefix="", info=NULL, geno=NULL)
x |
a |
chr.prefix |
prefix to add to seqlevels |
info |
which INFO fields to return |
geno |
which GENO fields to return |
Coerces a SeqVarGDSClass object to a
VCF-class object.
Row names correspond to the variant.id. info
and
geno
specify the 'INFO' and 'GENO' (FORMAT) fields to
return, respectively. If not specified, all fields are returned;
if 'NA' no fields are returned. Use seqSetFilter
prior to calling seqAsVCF
to specify samples and variants to
return.
The VariantAnnotation package should be loaded to explore this object.
A CollapsedVCF
object.
Stephanie Gogarten, Xiuwen Zheng
gds <- seqOpen(seqExampleFileName("gds")) ## Not run: library(VariantAnnotation) seqAsVCF(gds) ## End(Not run) seqClose(gds)