countSingletons {SeqVarTools} | R Documentation |
Count singleton variants for each sample
## S4 method for signature 'SeqVarGDSClass' countSingletons(gdsobj, use.names=FALSE)
gdsobj |
A |
use.names |
A logical indicating whether to assign variant IDs as names of the output vector. |
A singleton variant is a variant in which only one sample has a non-reference allele. For each sample, countSingletons
finds the number of variants for which that sample has the only non-reference allele.
A vector of the number of singleton variants per sample.
Stephanie Gogarten
SeqVarGDSClass
,
applyMethod
,
alleleFrequency
gds <- seqOpen(seqExampleFileName("gds")) head(countSingletons(gds)) seqClose(gds)