seqAsVCF: VariantAnnotation objects

In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

VariantAnnotation objects

Description

Create a VCF-class object

Usage

seqAsVCF(x, chr.prefix="", info=NULL, geno=NULL)

Arguments

x	a SeqVarGDSClass object
chr.prefix	prefix to add to seqlevels
info	which INFO fields to return
geno	which GENO fields to return

Details

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.

Value

A CollapsedVCF object.

Author(s)

Stephanie Gogarten, Xiuwen Zheng

See Also

VCF-class

Examples

gds <- seqOpen(seqExampleFileName("gds"))

## Not run: 
library(VariantAnnotation)
seqAsVCF(gds)

## End(Not run)

seqClose(gds)

zhengxwen/SeqArray documentation built on Dec. 14, 2024, 8:36 p.m.