utils.hwe

-- a genlight object containting the SNP profiles for a population [Required]

-- level of significance [Default 0.05]

prob

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

verbose

Calculates the probabilities of agreement with H-W equilibrium based on observed
frequencies of reference homozygotes, heterozygotes and alternate homozygotes. 
Uses the exact calculations contained in function utils.prob.hwe() as developed by
Wigginton, JE, Cutler, DJ, and Abecasis, GR.

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

utils.hwe: Calculates departure from Hardy-Weinberg Equilibrium. Utility script not meant for end users.

Description

Usage

Arguments

Value