transform_geno: Transform genotypes

In DominikMueller64/LDtools: Tools for Linkage Disequilibrium Analysis

Description

Transform genotypes from two-letter coding to numeric coding.

Usage

transform_geno(geno, sep = "/", check = TRUE)

Arguments

geno	A character matrix containing the genotypes.
sep	A character string use to split the genotypes in geno.
check	Should checks be performed?

Details

A genotype must consist of a sequence of three characters, where the mittle character is the seperator as specified in sep. Recoding is performed based on the major allele at the respective locus, i.e., if for instance the major allele is "A", the recoded genotypes of "A/A", "A/B", "B/A" and "B/B" will be, 2, 1, 1, 0, given sep = "/".

Value

A numeric matrix of the same dimensions as geno containing the recoded genotypes.

Author(s)

Dominik Mueller ([e-mail])

Examples

geno <- structure(c("A/G", "G/A", "A/A", NA, "A/A", "G/G", NA, "G/G",
                    "G/G", "A/A", "G/G", NA, "C/C", "C/C", "C/A", NA, "C/C", "C/C"),
                 .Dim = c(6L, 3L))
transform_geno(geno, sep = '/')

DominikMueller64/LDtools documentation built on May 6, 2019, 2:51 p.m.