qtl2 (version 0.36)

calc_sdp: Calculate strain distribution pattern from SNP genotypes

Description

Calculate the strain distribution patterns (SDPs) from the strain genotypes at a set of SNPs.

Usage

calc_sdp(geno)

Value

A vector of strain distribution patterns: integers between 1 and \(2^n - 2\) where \(n\) is the number of strains, whose binary representation indicates the strain genotypes.

Arguments

geno

Matrix of SNP genotypes, markers x strains, coded as 1 (AA) and 3 (BB). Markers with values other than 1 or 3 are omitted, and monomorphic markers, are omitted.

See Also

invert_sdp(), sdp2char()

Examples

x <- rbind(m1=c(3, 1, 1, 1, 1, 1, 1, 1),
           m2=c(1, 3, 3, 1, 1, 1, 1, 1),
           m3=c(1, 1, 1, 1, 3, 3, 3, 3))
calc_sdp(x)