isSNV: Flag single nucleotide variants

In smgogarten/SeqVarTools: Tools for variant data

Flag single nucleotide variants

Description

Flag single nucleotide variants

Usage

## S4 method for signature 'SeqVarGDSClass'
isSNV(gdsobj, biallelic=TRUE)

Arguments

gdsobj	A SeqVarGDSClass object with VCF data.
biallelic	A logical indicating whether only biallelic SNVs are considered.

Details

If biallelic=TRUE, a variant is considered a single nucleotide variant (SNV) if there is one reference allele and one alternate allele, each one base in length. If biallelic=FALSE, there may be multiple alternate alleles, each one base in length.

Setting biallelic=TRUE is considerably faster for large data sets.

Value

A logical vector indicating which variants are SNVs.

Author(s)

Stephanie Gogarten

See Also

SeqVarGDSClass, allele-methods, applyMethod

Examples

gds <- seqOpen(seqExampleFileName("gds"))
table(isSNV(gds))
seqClose(gds)

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