isVariant: Locate variant samples across sites
In SeqVarTools: Tools for variant data

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

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

1 2	## S4 method for signature 'SeqVarGDSClass' isVariant(gdsobj, use.names=FALSE, parallel=FALSE)

`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.

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.

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

Stephanie Gogarten

SeqVarGDSClass, applyMethod, getGenotype

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)