exactHWEDS: Hardy-Weinberg Equilibrium testing
In isglobal-brge/dsOmics: DataSHIELD server site Omic functions

exactHWEDS

R Documentation

Hardy-Weinberg Equilibrium testing

Description

This function performs exact Hardy-Weinberg Equilibrium testing (using Fisher's Test) over a selection of SNPs. It also counts genotype, calculates allele frequencies, and calculates inbreeding coefficients.

Usage

exactHWEDS(
  genoData,
  chromosome,
  geno.counts,
  block.size,
  permute,
  controls_column
)

Arguments

`genoData`	`GenotypeData` object
`chromosome`	`character` Chromosome to study. `"all"` to study all available chromosomes
`geno.counts`	`bool` if `TRUE`, genotype counts are returned in the output data.frame
`block.size`	`numeric` number of SNPs to read in at once
`permute`	`bool` logical indicator for whether to permute alleles before calculations
`controls_column`	`character` If specified, the control individuals found on this column (specified by the encoding `1`) will be excluded when calculating the HWE.