gl.report.secondaries

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

<p>SNP datasets generated by DArT include fragments with more than one SNP (that is, with secondaries) and record them separately with the same CloneID (=AlleleID).
These multiple SNP loci within a fragment are likely to be linked, and so you may wish to remove secondaries.
This script reports duplicate loci.</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.secondaries: Report loci containing secondary SNPs in a genlight {adegenet} object

Description

Usage

Arguments

Value

Examples