InbreedingFromHindHe: Estimate Inbreeding from Hind/He for a Given Ploidy

In lvclark/polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Estimate Inbreeding from Hind/He for a Given Ploidy

Description

After running HindHe and examining the distribution of values across taxa and loci, InbreedingFromHindHe can be used to estimate the inbreeding statistic F from the median or mode value of H_{ind}/H_E. The statistic estimated encompasses inbreeding from all sources, including population structure, self-fertilization, and preferential mating among relatives. It is intended to be used as input to the process_isoloci.py script.

Usage

InbreedingFromHindHe(hindhe, ploidy)

Arguments

hindhe	A value for H_{ind}/H_E. It should generally range from zero to one.
ploidy	A single integer indicating the ploidy of the population.

Value

A number indicating the inbreeding statistic F. This is calculated as:

1 - hindhe * ploidy / (ploidy - 1)

Author(s)

Lindsay V. Clark

See Also

HindHe, ExpectedHindHe, readProcessSamMulti, readProcessIsoloci

Examples

InbreedingFromHindHe(0.5, 2)
InbreedingFromHindHe(0.4, 2)
InbreedingFromHindHe(0.5, 4)

lvclark/polyRAD documentation built on June 14, 2025, 10:08 p.m.