filter.hwe: Filter markers by Hardy-Weinberg equilibrium

Description Usage Arguments Value References

View source: R/filter.hwe.R

Description

This function tests markers for Hardy-Weinberg equilibrium (HWE) and removes markers that are significantly out of HWE.

Usage

1
filter.hwe(data.obj, geno.obj, p.thresh = 1e-6, run.parallel = TRUE, n.cores = 2)

Arguments

data.obj

The object in which all results are stored. See read.population.

geno.obj

The object in which the genotype object is stored.

p.thresh

The p value below which markers are considered out of HWE.

run.parallel

A logical value to indicate whether to run the process in parallel.

n.cores

An integer specifying the number of cores to be used in parallel processing.

Value

This function returns the data object with the marker information pared down to only those markers in HWE.

References

Add reference for HWE. Hartl and Clark?


cape documentation built on May 29, 2017, 4:49 p.m.