gl.report.repavg

<p>-- name of the genlight object containing the SNP data [required]</p>

<p>SNP datasets generated by DArT have in index, RepAvg, generated by reproducing the data independently for 30
RepAvg is the proportion of alleles that give a reproducible result, averaged over both alleles for each locus.</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

gl.report.repavg: Report summary of RepAvg, reproducibility averaged over both alleles for each locus in a genlight adegenet object

Description

Usage

Arguments

Value

Examples