gl.report.overshoot

-- name of the genlight object [required]

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

verbose

This function checks the position of the SNP within the trimmed sequence tag and identifies those for which the SNP position is outside
the trimmed sequence tag. This can happen, rarely, when the sequence containing the SNP resembles the adaptor.

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.overshoot: Reports loci for which the SNP has been trimmed from the sequence tag along with the adaptor

Description

Usage

Arguments

Value

Details

Examples