reformat_chrX_genotypes: reformat chrX genotypes for males to hemizygous

Description Usage Arguments Value

View source: R/alleles_ddd.R

Description

Female chrX genotypes are untouched, as are genotypes on autosomal chromosomes. Males with heterozygous chrX genotypes are left unchanged, as we cannot be sure which genotype is correct. Possibly they should be removed. We also do not alter genotypes within pseduo-autosomal regions.

Usage

1
reformat_chrX_genotypes(vars, geno, ddd_parents)

Arguments

vars

seqminer::readVCFToListByRange output, list of values, which includes a genotype matrix as "GT", and sample IDs as sampleId.

geno

dataframe of biallelic genotypes, one column per individual

ddd_parents

information about DDD individuals, including sex

Value

dataframe of variants, where male allosomal chrX genotypes have been converted to hemizygous genotypes (e.g. "0/0" -> "0").


jeremymcrae/recessiveStats documentation built on May 17, 2017, 6:09 p.m.