Fij_core

Computes partial inbreeding coefficients, Fi(j).
A coefficient Fi(j) can be read as the probability of individual i being
homozygous for alleles derived from ancestor j

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

Fij_core function

<dl><dt>ped</dt>
<dd>A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.</dd>
<dt>ancestors</dt>
<dd>Vector of the identities to be assumed as founder ancestors.</dd>
<dt>ancestors_idx</dt>
<dd>Index of ancestors.</dd>
<dt>Fi</dt>
<dd>Vector of inbreeding coefficients.</dd>
<dt>mapa</dt>
<dd>Map of ancestors</dd>
<dt>ncores</dt>
<dd>Number of cores to use for parallel computing (default = 1)</dd>
<dt>genedrop</dt>
<dd>Enable genedrop simulation</dd>
<dt>seed</dt>
<dd>Sets a seed for the random number generator.</dd></dl>

Arguments

Partial inbreeding coefficient (core function) — Fij_core

<dl>

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


<dt>ancestors</dt>
<dd>Vector of the identities to be assumed as founder ancestors.</dd>


<dt>ancestors_idx</dt>
<dd>Index of ancestors.</dd>


<dt>Fi</dt>
<dd>Vector of inbreeding coefficients.</dd>


<dt>mapa</dt>
<dd>Map of ancestors</dd>


<dt>ncores</dt>
<dd>Number of cores to use for parallel computing (default = 1)</dd>


<dt>genedrop</dt>
<dd>Enable genedrop simulation</dd>


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

</dl>

Fij_core: Partial inbreeding coefficient (core function)

Description

Usage

Value

Arguments