GenicVarianceMatrixFactory#

class pybrops.model.vmat.fcty.GenicVarianceMatrixFactory.GenicVarianceMatrixFactory[source]#

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)[source]#

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