ancestors

Returns a boolean vector indicating what individuals are suitable for purging analyses, given a measure of fitness.
Individuals with NA values of fitness, and that do not have descendants with non-NA fitness values, are excluded.

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

ancestors function

<dl><dt>ped</dt>
<dd>A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.</dd>
<dt>reference</dt>
<dd>A string naming a column indicating whether individuals belong to the reference population or not. Column must be boolean or coercible to boolean type.</dd>
<dt>rp_idx</dt>
<dd>Vector containing the indexes of individuals of the RP</dd>
<dt>nboot</dt>
<dd>Number of bootstrap iterations (for computing Ng).</dd>
<dt>seed</dt>
<dd>Sets a seed for the random number generator.</dd>
<dt>skip_Ng</dt>
<dd>Skip Ng computation or not (FALSE by default).</dd></dl>

Arguments

Individuals to be evaluated in purging analyses — ancestors

<dl>

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


<dt>reference</dt>
<dd>A string naming a column indicating whether individuals belong to the reference population or not. Column must be boolean or coercible to boolean type.</dd>


<dt>rp_idx</dt>
<dd>Vector containing the indexes of individuals of the RP</dd>


<dt>nboot</dt>
<dd>Number of bootstrap iterations (for computing Ng).</dd>


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


<dt>skip_Ng</dt>
<dd>Skip Ng computation or not (FALSE by default).</dd>

</dl>

ancestors: Individuals to be evaluated in purging analyses

Description

Usage

Value

Arguments