utils.recalc.maf

The locus metadata supplied by DArT does not have MAF included, so it is
calculated and added to the locus.metadata by this script. The minimum allele
frequency will change when some individuals are removed from the dataset.
This script recalculates the MAF and places these recalculated values in the
 appropriate place in the genlight object.

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.recalc.maf function

<dl><dt>x</dt>
<dd>Name of the genlight object containing the SNP data [required].</dd>
<dt>verbose</dt>
<dd>Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
progress log; 3, progress and results summary; 5, full report [default 2].</dd></dl>

Arguments

Custodian: Luis Mijangos (Post to
<a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>)

Author

A utility script to recalculate the minor allele frequency by locus,
typically after some populations have been deleted — utils.recalc.maf

<dl>

<dt>x</dt>
<dd>Name of the genlight object containing the SNP data [required].</dd>


<dt>verbose</dt>
<dd>Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
progress log; 3, progress and results summary; 5, full report [default 2].</dd>

</dl>

Custodian: Luis Mijangos (Post to
<a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>)

utils.recalc.maf: A utility script to recalculate the minor allele frequency by locus, typically after some populations have been deleted

Description

Usage

Value

Arguments

Author

See Also

Examples