flip_alleles: Flip alleles in a minor-allele dosage matrix

In etnite/bwardr: Brian Ward personal R package

Flip alleles in a minor-allele dosage matrix

Description

Flip alleles in a minor-allele dosage matrix

Usage

flip_alleles(genmat, snps = "rows")

Arguments

genmat	A numeric matrix of SNPs x individuals, with SNPs encoded as 0, 1, 2. Can be in either orientation (SNPs x individuals or individuals x SNPs)
snps	Either "rows" to indicate that SNPs are in rows and individuals are in columns, or "cols" to indicate the SNPs are in columns and individuals are in rows

Details

SNP data is often stored in numeric matrices in minor-allele dosage format, where 0 indicates no copies of the minor allele (i.e. homozygous for the major allele), 1 indicates 1 copy of the minor allele (i.e. heterozygous), and 2 indicates 2 copies of the minor allele (i.e. homozygous for the minor allele). However, there are situations in which the alleles get "flipped" between major vs. minor (e.g. when subsetting or filtering genotypic data). In addition, SNPs may be numerically encoded in various ways, e.g. by encoding the allele in the reference genome as 0, and the alternate allele as 2. flip_alleles() is intended to selectively "flip" SNPs into the proper minor-allele dosage orientation.

Value

List containing the following elements:

• dosmat - NumericSNP matrix in minor-allele dosage format

• flipped_loci - Vector listing markers for which alleles were flipped

See Also

gt2num

etnite/bwardr documentation built on Jan. 6, 2023, 7:12 a.m.