Computes the ancestral inbreeding coefficient (Fa).
This is the probability that an allele has been in homozygosity in at least one ancestor (Ballou 1997).
A genedrop approach is included to compute unbiased estimates of Fa (Baumung et al. 2015).

Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load.
In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included.
See López-Cortegano E. (2021) <doi:10.1093/bioinformatics/btab599>.

Eugenio L<c3><b3>pez-Cortegano

purgeR

Inbreeding-Purging Estimation in Pedigreed Populations

Eugenio López-Cortegano

Fa function

<dl><dt>ped</dt>
<dd>A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.</dd>
<dt>Fi</dt>
<dd>Vector of inbreeding coefficient values</dd>
<dt>name_to</dt>
<dd>A string naming the new output column.</dd>
<dt>genedrop</dt>
<dd>Number of genedrop iterations to run. If set to zero (as default), Ballou's Fa is computed.</dd>
<dt>seed</dt>
<dd>Sets a seed for the random number generator.</dd></dl>

Arguments

Ancestral inbreeding coefficient — Fa

<dl>

<dt>ped</dt>
<dd>A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.</dd>


<dt>Fi</dt>
<dd>Vector of inbreeding coefficient values</dd>


<dt>name_to</dt>
<dd>A string naming the new output column.</dd>


<dt>genedrop</dt>
<dd>Number of genedrop iterations to run. If set to zero (as default), Ballou's Fa is computed.</dd>


<dt>seed</dt>
<dd>Sets a seed for the random number generator.</dd>

</dl>

Fa: Ancestral inbreeding coefficient

Description

Usage

Value

Arguments

References