seqAsVCF: VariantAnnotation objects

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/asVCF.R

Description

Create a VCF-class object

Usage

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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

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

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

## End(Not run)

seqClose(gds)

SeqArray documentation built on Nov. 17, 2018, 6 p.m.