pm: Probability Matrix

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

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)

hsphase documentation built on May 29, 2024, 2:20 a.m.