convert.alleles.to.pgs.dosage: Convert alleles to dosage

In ApplyPolygenicScore: Utilities for the Application of a Polygenic Score to a VCF

Convert alleles to dosage

Description

Convert genotype calls in the form of witten out alleles (e.g. 'A/T') to dosages (0, 1, 2) based on provided risk alleles from a PGS.

Usage

convert.alleles.to.pgs.dosage(called.alleles, risk.alleles)

Arguments

called.alleles	A vector of genotypes in allelic notation separated by a slash or pipe.
risk.alleles	A vector of risk alleles from a polygenic score corresponding to each genotype (by locus) in called.alleles.

Value

A vector of dosages corresponding to each genotype in called.alleles. Hemizygous genotypes (one allele e.g. 'A') are counted as 1.

Examples

called.alleles <- c('A/A', 'A/T', 'T/T');
risk.alleles <- c('T', 'T', 'T');
convert.alleles.to.pgs.dosage(called.alleles, risk.alleles);

ApplyPolygenicScore documentation built on April 4, 2025, 12:18 a.m.