chromWithPAR {SeqVarTools} | R Documentation

## Identify pseudoautosomal region

### 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

[Package SeqVarTools version 1.30.0 Index]