exactHWEDS: Hardy-Weinberg Equilibrium testing

View source: R/exactHWEDS.R

exactHWEDSR 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.


isglobal-brge/dsOmics documentation built on Nov. 11, 2024, 4:18 a.m.