geno1to2: convert genotype matrix from 1-column 2-column

In haplo.stats: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

convert genotype matrix from 1-column 2-column

Description

convert 1-column genotype matrix to 2-column genotype matrix, converting from a minor allele count (0,1,2) to (1/1, 1/2, 2/2) where 2 is the minor allele. (not supported for x-linked markers)

Usage

geno1to2(geno, locus.label=NULL)

Arguments

geno	1-column representation of genotype matrix for 2-allele loci. Values are 0, 1, or 2, usually the count of minor alleles
locus.label	Vector of labels for loci, If a locus name is "A", its columns will be "A.1" and "A.2"

Value

a 2-column genotype matrix

Examples

geno1 <- matrix(c(0,0,1,
                  1,0,2,
                  2,1,0), ncol=3, byrow=TRUE)
geno1to2(geno1, locus.label=c("A", "B", "C"))

## demonstrate how NA and 3 will be coded
geno1[1,3] <- NA
geno1[1,1] <- 3
geno1to2(geno1)

haplo.stats documentation built on May 29, 2024, 9:53 a.m.