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].

verbose

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

Arthur Georges

Jose L. Mijangos

Carlo Pacioni

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

utils.recalc.maf function

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

A utility script to recalculate the minor allele frequency by locus,
typically after some populations have been deleted

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

Description

Usage

Arguments

Value

See Also

Examples