isVariant {SeqVarTools} | R Documentation |
Locate which samples are variant for each site in a GDS object
## S4 method for signature 'SeqVarGDSClass' isVariant(gdsobj, use.names=FALSE)
gdsobj |
A |
use.names |
A logical indicating whether to assign sample and variant IDs as dimnames of the resulting matrix. |
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)