as.segsites.GENOME

Using this function, you can convert genetic data imported with the package
PopGenome into coala's segsites format. See <code>as.segsites</code>
for general information on converting genetic data for coala.

Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results (Staab, Metzler,
2016 <doi:10.1093/bioinformatics/btw098>).
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.
Coala provides functions for calculating certain summary statistics, which
can also be applied to actual biological data.
One possibility to import data is through the 'PopGenome' package
(<https://github.com/pievos101/PopGenome>).

Dirk Metzler

coala

A Framework for Coalescent Simulation

Paul Staab

Jorge E. Amaya Romero

as.segsites.GENOME function

<dl><dt>data</dt>
<dd>The <code>GENOME</code> data from PopGenome.</dd>
<dt>only_synonymous</dt>
<dd>Only import synonymous SNPs if set to <code>TRUE</code>.
This requires that PopGenome knows where coding regions are., e.g.
by using gff files.</dd>
<dt>...</dt>
<dd>Ignored.</dd></dl>

Arguments

Convert PopGenome Data into Coala's Format — as.segsites.GENOME

<dl>

<dt>data</dt>
<dd>The <code>GENOME</code> data from PopGenome.</dd>


<dt>only_synonymous</dt>
<dd>Only import synonymous SNPs if set to <code>TRUE</code>.
This requires that PopGenome knows where coding regions are., e.g.
by using gff files.</dd>


<dt>...</dt>
<dd>Ignored.</dd>

</dl>

as.segsites.GENOME: Convert PopGenome Data into Coala's Format

Description

Usage

Arguments

Details

See Also