getFst

This function computes FST according to Hudson's estimator following Bathia.
Note that the frequencies for the two populations should be entered as
separate inputs.

internal

Provides functions to simulate Pool-seq data under models of
demographic formation and to import Pool-seq data from real populations.
Implements two ABC algorithms for performing parameter estimation and
model selection using Pool-seq data. Cross-validation can also be
performed to assess the accuracy of ABC estimates and model choice.
Carvalho et al., (2022) <doi:10.1111/1755-0998.13834>.

João Carvalho

poolABC

Approximate Bayesian Computation with Pooled Sequencing Data

Vítor Sousa

getFst function

<dl><dt>freq1</dt>
<dd>is a numeric vector with the allele frequencies for population<ol>
<li>Each entry of the vector should be a different site.</li>
</ol></dd>
<dt>freq2</dt>
<dd>is a numeric vector with the allele frequencies for population
2. Each entry of the vector should be a different site.</dd>
<dt>ss1</dt>
<dd>vector with the sample size for population 1. Each entry of the
vector should contain the number of reads for a different site.</dd>
<dt>ss2</dt>
<dd>vector with the sample size for population 2. Each entry of the
vector should contain the number of reads for a different site.</dd></dl>

Arguments

Calculate FST — getFst

<dl>

<dt>freq1</dt>
<dd>is a numeric vector with the allele frequencies for population<ol>
<li>Each entry of the vector should be a different site.</li>
</ol></dd>


<dt>freq2</dt>
<dd>is a numeric vector with the allele frequencies for population
2. Each entry of the vector should be a different site.</dd>


<dt>ss1</dt>
<dd>vector with the sample size for population 1. Each entry of the
vector should contain the number of reads for a different site.</dd>


<dt>ss2</dt>
<dd>vector with the sample size for population 2. Each entry of the
vector should contain the number of reads for a different site.</dd>

</dl>

getFst: Calculate FST

Description

Usage

Value

Arguments

Details