haplo.fix

This function applies a correction for the situations where <code>scrm::scrm()</code>
does not produce a single polymorphic site for a given locus. In this
situation, two artificial sites are created at that locus. All individuals
are assumed to be homozygous for the reference allele at those sites.

internal

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

haplo.fix function

<dl><dt>haplotypes</dt>
<dd>a list of haplotypes obtained from the simulations done
with <code>scrm::scrm()</code>. Each entry of the list is a matrix that corresponds to
a given locus. At each matrix, each column is a different site and each row
is a different haplotype.</dd>
<dt>nHap</dt>
<dd>an integer representing the total number of haplotypes simulated.</dd></dl>

Arguments

Create invariable sites — haplo.fix

<dl>

<dt>haplotypes</dt>
<dd>a list of haplotypes obtained from the simulations done
with <code>scrm::scrm()</code>. Each entry of the list is a matrix that corresponds to
a given locus. At each matrix, each column is a different site and each row
is a different haplotype.</dd>


<dt>nHap</dt>
<dd>an integer representing the total number of haplotypes simulated.</dd>

</dl>

haplo.fix: Create invariable sites

Description

Usage

Value

Arguments