imputedDosage: Get imputed dosage

In smgogarten/SeqVarTools: Tools for variant data

Get imputed dosage

Description

Get matrix of imputed dosage values from a GDS object

Usage

## S4 method for signature 'SeqVarGDSClass'
imputedDosage(gdsobj, dosage.field="DS", use.names=TRUE)

Arguments

gdsobj	A SeqVarGDSClass object with VCF data.
dosage.field	The name of the dosage field in the GDS object (will be prepended with "annotation/format").
use.names	A logical indicating whether to assign sample and variant IDs as dimnames of the resulting matrix.

Details

Reads dosage from the dosage-specific field in the GDS object, rather than counting alleles from called genotypes.

Only one dosage value per variant is allowed; the method will return an error if multiple dosages are present for a single variant.

Value

A numeric matrix of dosage values with dimensions [sample,variant].

Author(s)

Stephanie Gogarten

See Also

refDosage, altDosage

Examples

# convert VCF to GDS keeping dosage field
vcffile <- system.file("extdata", "gl_chr1.vcf", package="SeqVarTools")
gdsfile <- tempfile()
seqVCF2GDS(vcffile, gdsfile, fmt.import="DS", storage.option="ZIP_RA",
           verbose=FALSE)

gds <- seqOpen(gdsfile)
dos <- imputedDosage(gds)
head(dos)
seqClose(gds)
unlink(gdsfile)

smgogarten/SeqVarTools documentation built on July 4, 2023, 2:34 a.m.