countSingletons: Count singletons

In smgogarten/SeqVarTools: Tools for variant data

Count singletons

Description

Count singleton variants for each sample

Usage

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

Arguments

gdsobj	A SeqVarGDSClass object with VCF data.
use.names	A logical indicating whether to assign variant IDs as names of the output vector.

Details

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.

Value

A vector of the number of singleton variants per sample.

Author(s)

Stephanie Gogarten

See Also

SeqVarGDSClass, applyMethod, alleleFrequency

Examples

gds <- seqOpen(seqExampleFileName("gds"))
head(countSingletons(gds))
seqClose(gds)

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