filter_variants_by_standard_chromosomes: Filter variants by standard human chromosomes.
In gwasrapidd: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

filter_variants_by_standard_chromosomes

R Documentation

Filter variants by standard human chromosomes.

Description

This function filters a variants object by standard human chromosomes, i.e., 1–22, X and Y. In addition to these chromosomes, some variants retrieved from the GWAS Catalog might be also mapped to non-standard locations, such as GRC assembly patches, haplotype (HAPs) or pseudo autosomal regions (PARs). When this happens the main table variants includes rows for these cases too. This function removes these.

Usage

filter_variants_by_standard_chromosomes(
  s4_variants,
  chromosomes = c(seq_len(22), "X", "Y", "MT")
)

Arguments

`s4_variants`	An object of class variants.
`chromosomes`	A character vector of valid chromosome names. Default is autosomal chromosomes 1 thru 22 and, X, Y, and MT.