DenseUnphasedGenotyping#

class pybrops.breed.prot.gt.DenseUnphasedGenotyping.DenseUnphasedGenotyping(**kwargs)[source]#

Bases: GenotypingProtocol

Class implementing unphased genotyping for dense genotype matrices. This converts a DensePhasedGenotypeMatrix to a DenseGenotypeMatrix containing genotype values.

Constructor for the concrete class DenseUnphasedGenotyping.

Perform unphased genotyping on a genome.

Parameters:: kwargs (dict) – Additional keyword arguments.

Methods

genotype

Genotype a genome.

genotype(pgmat, miscout=None, **kwargs)[source]#

Genotype a genome. Returned matrix is in {0,1,2} format.

Parameters:

pgmat (PhasedGenotypeMatrix) – A phased genotype matrix representing the whole simulated genome.
miscout (dict, None) – Pointer to a dictionary for miscellaneous user defined output. If dict, write to dict (may overwrite previously defined fields). If None, user defined output is not calculated or stored.
kwargs (dict) – Additional keyword arguments.

Returns:

out – A DenseGenotypeMatrix of genotyped individuals.

Return type:

GenotypeMatrix