GenicVarianceMatrixFactory

class pybrops.model.vmat.fcty.GenicVarianceMatrixFactory.GenicVarianceMatrixFactory

Bases: object

Abstract class for GenicVarianceMatrix factory classes.

The purpose of this abstract interface is to provide functionality for:

1. Construction of genetic variance matrices.

Methods

from_gmod

Estimate genetic variances from a GenomicModel and PhasedGenotypeMatrix.

abstract from_gmod(gmod, pgmat, nprogeny, **kwargs)

Estimate genetic variances from a GenomicModel and PhasedGenotypeMatrix.

Parameters:

• gmod (GenomicModel) – GenomicModel with which to estimate genetic variances.

• pgmat (PhasedGenotypeMatrix) – Input genomes to use to estimate genetic variances.

• ncross (int) – Number of cross patterns to simulate for genetic variance estimation.

• nprogeny (int) – Number of progeny to simulate per cross to estimate genetic variance.

• nself (int) – Number of selfing generations post-cross pattern before ‘nprogeny’ individuals are simulated.

• gmapfn (GeneticMapFunction) – Genetic map function with which to calculate recombination probabilities.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A matrix of genetic variance estimations.

Return type:

GenicVarianceMatrix