isVariant: Locate variant samples across sites

In smgogarten/SeqVarTools: Tools for variant data

Locate variant samples across sites

Description

Locate which samples are variant for each site in a GDS object

Usage

## S4 method for signature 'SeqVarGDSClass'
isVariant(gdsobj, use.names=FALSE, parallel=FALSE)

Arguments

gdsobj	A SeqVarGDSClass object with VCF data.
use.names	A logical indicating whether to assign sample and variant IDs as dimnames of the resulting matrix.
parallel	Logical, numeric, or other value to control parallel processing; see seqParallel for details.

Details

Each sample/site cell of the resulting matrix is TRUE if the genotype at that location for that sample contains an alternate allele. A genotype of "0/0" is not variant, while genotypes "0/1", "1/0", "0/2", etc. are variant.

Value

A logical matrix with dimensions [sample,site] which is TRUE for cells where the genotype contains an alternate allele.

Author(s)

Stephanie Gogarten

See Also

SeqVarGDSClass, applyMethod, getGenotype

Examples

gds <- seqOpen(seqExampleFileName("gds"))
variant.id <- seqGetData(gds, "variant.id")
sample.id <- seqGetData(gds, "sample.id")
applyMethod(gds, isVariant, variant.id[1:5], sample.id[1:10])
applyMethod(gds, isVariant, variant.id[1:5], sample.id[1:10], use.names=TRUE)
seqClose(gds)

smgogarten/SeqVarTools documentation built on Sept. 15, 2024, 1:08 p.m.