chromWithPAR: Identify pseudoautosomal region

In SeqVarTools: Tools for variant data

Description

Flag single nucleotide variants

Usage

## S4 method for signature 'SeqVarGDSClass'
chromWithPAR(gdsobj, genome.build=c("hg19", "hg38"))

Arguments

gdsobj	A SeqVarGDSClass object with VCF data.
genome.build	A character sting indicating genome build.

Details

The pseudoautosomal region (PAR) should be treated like the autosomes for purposes of calculating allele frequency. This method returns a vector where sex chromosome variants are labeled wither "X", "Y", or "PAR".

Value

A character vector of chromosome, with values "PAR" for the pseudoautosomal region.

Author(s)

Stephanie Gogarten

References

https://www.ncbi.nlm.nih.gov/grc/human

SeqVarTools documentation built on Nov. 22, 2020, 2 a.m.