haplomat#

pybrops.core.util.haplo.haplomat(nhaploblk, genomemat, genpos, chrgrp_stix, chrgrp_spix, chrgrp_len, u_a)[source]#

Calculate a haplotype matrix from a genome matrix and model.

Parameters:

nhaploblk (Integral) – Number of haplotype blocks
genomemat (numpy.ndarray) –
A genome matrix of shape (m,n,p).

Where:
- m is the number of chromsome phases.
- n is the number of individuals.
- p is the number of markers.
genpos (numpy.ndarray) –
Array of shape (p,) containing genetic positions of markers across the genome.

Where:
- p is the number of markers.
Input contraints:
- Must be sorted in ascending order.
- Must be grouped based on chromosome. The chromosome boundary start and stop indices must be provided in chrgrp_stix and chrgrp_spix, respectively.
chrgrp_stix (numpy.ndarray) –
Chromosome boundary start indices array of shape (c,).

Where:
- c is the number of chromosomes.
chrgrp_spix (numpy.ndarray) –
Chromosome boundary stop indices array of shape (c,).

Where:
- c is the number of chromosomes.
chrgrp_len (numpy.ndarray) –
Chromosome length array of shape (c,).

Where:
- c is the number of chromosomes.
u_a (numpy.ndarray) –
Array of shape (p,t) containing additive marker effect estimates.

Where:
- p is the number of markers.
- t is the number of traits.

Returns:

out – A haplotype effect matrix of shape (m,n,b,t).

Where:

Return type:

numpy.ndarray