calc_jsfs

Calculates the Joint Site Frequency Spectrum

internal

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

calc_jsfs function

<dl><dt>segsites_list</dt>
<dd>List of segregating sites</dd>
<dt>ind_per_pop</dt>
<dd>A list of integer vector, where each entry gives the
index of the haploids that belong the corresponding population.</dd></dl>

Arguments

Author

Calculates the Joint Site Frequency Spectrum — calc_jsfs

<dl>

<dt>segsites_list</dt>
<dd>List of segregating sites</dd>


<dt>ind_per_pop</dt>
<dd>A list of integer vector, where each entry gives the
index of the haploids that belong the corresponding population.</dd>

</dl>

calc_jsfs: Calculates the Joint Site Frequency Spectrum

Description

Usage

Value

Arguments

Author