utils.recalc.maf

-- name of the genlight object containing the SNP data [required]

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

The locus metadata supplied by DArT does not have MAF included, so it is calculated and
added to the locus.metadata by this script. The minimum allele frequency will change when
some individuals are removed from the dataset. This script recalculates the MAF and 
places these recalculated values in the appropriate place in the genlight object.

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

utils.recalc.maf: A utility script to recalculate the the minor allele frequency by locus, typically after some populations have been deleted

Description

Usage

Arguments

Value

Examples