SeqVarTools (version 1.10.0)

isVariant: Locate variant samples across sites

Description

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

Usage

"isVariant"(gdsobj, use.names=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.

Value

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

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.

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)