DenseMaskedUnphasedGenotyping

class pybrops.breed.prot.gt.DenseMaskedUnphasedGenotyping.DenseMaskedUnphasedGenotyping(invert=False, **kwargs)

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 DenseMaskedUnphasedGenotyping.

Perform unphased genotyping on a genome.

Parameters:

• invert (bool) – Whether to invert the variant mask when genotyping. If False, then variants with mask values == True are genotyped. If True, then variants with mask values == False are genotyped.

• kwargs (dict) – Additional keyword arguments.

Methods

genotype

Genotype a genome.

Attributes

invert

Whether to invert the variant mask when genotyping.

genotype(pgmat, miscout=None, **kwargs)

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

property invert: bool

Whether to invert the variant mask when genotyping.