pm {hsphase}

Probability Matrix

Description

Creates a recombination matrix based on the blocking structure.

Usage

pm(blockMatrix, method = "constant") 

Arguments

blockMatrix

matrix blocking structure (Output of bmh)

method

character method for creating the recombination matrix

Details

This function finds the recombination between two consecutive sites, and marks the recombination site with a 1; if there are unknown sites between two blocks it will also mark these sites with a 1 (constant method) or 1 divided by number of unknown site (relative method).

Examples

genotype <- matrix(c(
0,2,0,1,0,
2,0,1,2,2,
2,2,1,0,2,
2,2,1,1,1,
0,0,2,1,0), ncol = 5, byrow = TRUE) # each row contains the SNP of individuals

(result <- bmh(genotype))
pm(result)