utils.clumpp

Functions from package starmie for merging Q matrices from Structure runs
using the CLUMPP algorithms.

Functions are provided that facilitate the import and analysis of
'SNP' (single nucleotide polymorphism) and 'silicodart' (presence/absence) data.
The main focus is on data generated by 'DarT' (Diversity Arrays Technology),
however, data from other sequencing platforms can be used once 'SNP' or related
fragment presence/absence data from any source is imported. Genetic datasets
are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility,
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR' supports also the analysis of 3rd party software package
such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version
2.0.3 we also implemented simulation functions, that allow to forward simulate
'SNP' dynamics under different population and evolutionary dynamics.
Comprehensive tutorials and support can be found at our 'github' repository:
github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find
the information by typing citation('dartR') in the console.

Bernd Gruber

dartR

Importing and Analysing 'SNP' and 'Silicodart' Data Generated by
Genome-Wide Restriction Fragment Analysis

Arthur Georges

Jose L. Mijangos

Carlo Pacioni

Diana Robledo-Ruiz

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

utils.clumpp function

<dl><dt>Q_list</dt>
<dd>A list of of Q matrices.</dd>
<dt>method</dt>
<dd>The algorithm to use to infer the correct permutations. One of
'greedy' or 'greedyLargeK' or 'stephens'</dd>
<dt>iter</dt>
<dd>The number of iterations to use if running either 'greedy' or
'greedyLargeK'</dd></dl>

Arguments

Functions from package starmie for merging Q matrices from Structure runs
using the CLUMPP algorithms. — utils.clumpp

<dl>

<dt>Q_list</dt>
<dd>A list of of Q matrices.</dd>


<dt>method</dt>
<dd>The algorithm to use to infer the correct permutations. One of
'greedy' or 'greedyLargeK' or 'stephens'</dd>


<dt>iter</dt>
<dd>The number of iterations to use if running either 'greedy' or
'greedyLargeK'</dd>

</dl>

Functions from package starmie for merging Q matrices from Structure runs
using the CLUMPP algorithms.

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utils.clumpp: Functions from package starmie for merging Q matrices from Structure runs using the CLUMPP algorithms.

Description

Usage

Arguments