InbreedingFromHindHe

After running <code>HindHe</code> and examining the distribution of values
across taxa and loci, <code>InbreedingFromHindHe</code> 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 <code>process_isoloci.py</code> script.

 arith 

Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids. The genotype
probabilities, posterior mean genotypes, or most probable genotypes can then
be exported for downstream analysis. 'polyRAD' is described by Clark et al.
(2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker
filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>.
A variant calling pipeline for highly duplicated genomes is also included and
is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.

Lindsay V. Clark

polyRAD

Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids

U.S. National Science Foundation 

InbreedingFromHindHe function

<dl> <dt>hindhe</dt>
<dd>A value for \(H_{ind}/H_E\). It should generally range from zero to
one.</dd> <dt>ploidy</dt>
<dd>A single integer indicating the ploidy of the population.</dd></dl>

Arguments

Author

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

<dl>

 <dt>hindhe</dt>
<dd>A value for \(H_{ind}/H_E\). It should generally range from zero to
one.</dd>

 <dt>ploidy</dt>
<dd>A single integer indicating the ploidy of the population.</dd>

</dl>

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

Description

Usage

Value

Arguments

Author

See Also

Examples