utils.basic.stats

<p>A genlight object containing the SNP genotypes [required].</p>

<p>This is a re-implementation of <code>hierfstat::basics.stats</code> specifically 
 for genlight objects. Formula (and hence results) match exactly the original 
version of <code>hierfstat::basics.stats</code> (although Dstp and Fstp are not 
currently computed) but it is much faster.</p>

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, once SNP or related fragment presence/absence data from any source
is imported into a genlight object many of the functions can be used.
Functions are available for input and output of SNP and silicodart data, for
reporting on and filtering on various criteria (e.g. CallRate,
Heterozygosity, Reproducibility, maximum allele frequency). Advanced
filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg
equilibrium). Other functions are available for visualization after PCoA
(Principle Coordinate Analysis), or to facilitate transfer of data between
genlight/genind objects and newhybrids, related, phylip, structure,
faststructure packages.

Bernd Gruber

dartR

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

Arthur Georges

Jose L. Mijangos

Carlo Pacioni

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

utils.basic.stats function

Calculates mean observed heterozygosity, mean expected heterozygosity and Fis
 per locus, per population and Fst across all populations — utils.basic.stats

Calculates mean observed heterozygosity, mean expected heterozygosity and Fis
 per locus, per population and Fst across all populations

utils.basic.stats: Calculates mean observed heterozygosity, mean expected heterozygosity and Fis per locus, per population and Fst across all populations

Description

Usage

Arguments

Value

Examples