Ifreqs

Computes alternative allele frequencies from genotypes by dividing the total
number of alternative alleles by the total number of gene copies.

Simulates pooled sequencing data under a variety of conditions.
Also allows for the evaluation of the average absolute difference between allele frequencies
computed from genotypes and those computed from pooled data.
Carvalho et al., (2022) <doi:10.1101/2023.01.20.524733>.

João Carvalho

poolHelper

Simulates Pooled Sequencing Genetic Data

Vítor Sousa

Ifreqs function

<dl><dt>nDip</dt>
<dd>an integer representing the total number of diploid individuals
to simulate. Note that <code>scrm::scrm()</code> actually simulates haplotypes, so the
number of simulated haplotypes is double of this.</dd>
<dt>genotypes</dt>
<dd>a list of simulated genotypes, where each entry is a matrix
corresponding to a different locus. At each matrix, each column is a
different SNP and each row is a different individual.</dd></dl>

Arguments

Compute allele frequencies from genotypes — Ifreqs

<dl>

<dt>nDip</dt>
<dd>an integer representing the total number of diploid individuals
to simulate. Note that <code>scrm::scrm()</code> actually simulates haplotypes, so the
number of simulated haplotypes is double of this.</dd>


<dt>genotypes</dt>
<dd>a list of simulated genotypes, where each entry is a matrix
corresponding to a different locus. At each matrix, each column is a
different SNP and each row is a different individual.</dd>

</dl>

Ifreqs: Compute allele frequencies from genotypes

Description

Usage

Value

Arguments

Examples