qtl2convert (version 0.30)

find_unique_geno: Find the unique genotypes for each row of a genotype matrix

Description

For genotype data (markers x individuals) on a set of individuals, find the unique genotypes for each marker, provided that there are exactly two. (If more than two or fewer than two, return NAs.)

Usage

find_unique_geno(genotypes, na.strings = c("N", "H", "NA", ""), cores = 1)

Value

Matrix with two columns. Each row corresponds to a marker, and has the two unique genotypes, or NAs (if >2 or <2 unique genotypes).

Arguments

genotypes

Matrix of genotypes (markers x individuals)

na.strings

Genotypes to be considered as missing values.

cores

Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().

See Also

count_unique_geno(), encode_geno()

Examples

g <- rbind(c("NA", "A",  "A",  "A", "T"),
           c("NA", "NA", "NA", "A", "A"),
           c("A",  "A",  "T",  "G", "G"),
           c("C", "C",  "G",  "G", "NA"))
ug <- find_unique_geno(g)