as.segsites

This function can be used to convert the genomic data formats used in other
packages to calculate coala's segregating sites object. This is useful for
calculating the summary statistics of biological data using the
<code>calc_sumstats_from_data</code> function.

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 function

<dl><dt>data</dt>
<dd>The data object that is converted.</dd>
<dt>...</dt>
<dd>Additional arguments specific for the used package.</dd></dl>

Arguments

Convert genetic data to coala's internal format — as.segsites

<dl>

<dt>data</dt>
<dd>The data object that is converted.</dd>


<dt>...</dt>
<dd>Additional arguments specific for the used package.</dd>

</dl>

as.segsites: Convert genetic data to coala's internal format

Description

Usage

Value

Arguments

Details

See Also