utils.basic.stats

WARNING: UTILITY SCRIPTS ARE FOR INTERNAL USE ONLY AND SHOULD NOT BE USED BY
 END USERS AS THEIR USE OUT OF CONTEXT COULD LEAD TO UNPREDICTABLE OUTCOMES.

Facilitates 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.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
supports the installation of all packages in the 'dartRverse'.
If you want to cite 'dartR', you find the information by typing citation('dartR.base')
in the console.

Bernd Gruber

dartR.base

Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Arthur Georges

Jose L. Mijangos

Carlo Pacioni

Diana Robledo-Ruiz

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

Ching Ching Lau

utils.basic.stats function

<dl><dt>x</dt>
<dd>A genlight object containing the SNP genotypes [required].</dd></dl>

Arguments

Luis Mijangos and Carlo Pacioni (post to
<a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>)

Author

Calculates mean observed heterozygosity, mean expected heterozygosity 
and FIS per locus, per population and various population differentiation 
measures
 @family utilities — utils.basic.stats

<dl>

<dt>x</dt>
<dd>A genlight object containing the SNP genotypes [required].</dd>

</dl>

Luis Mijangos and Carlo Pacioni (post to
<a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>)

Calculates mean observed heterozygosity, mean expected heterozygosity 
and FIS per locus, per population and various population differentiation 
measures
 @family utilities

utils.basic.stats: Calculates mean observed heterozygosity, mean expected heterozygosity and FIS per locus, per population and various population differentiation measures @family utilities

Description

Usage

Value

Arguments

Author

Details

Examples