HWE.chisq {GeneticsBase}R Documentation

Hardy-Weinberg Equilibrium Significance test for a biallelic locus

Description

Hardy-Weinberg Equilibrium Significance test for a biallelic locus .

Usage

HWE.chisq(object,
          marker,
          simulate.p.value = TRUE,
          B = 10000, 
          founderOnly=TRUE, 
          ...)

Arguments

object a geneSet object.
marker marker name for the biallelic locus.
simulate.p.value a logical indicating whether to compute p-values by Monte Carlo simulation.
B an integer specifying the number of replicates used in the Monte Carlo test. Defaults to 10000.
founderOnly Indicates if only founders are used to do the test.
... Othere arguments used by the function chisq.test.

Value

The values of the function HWE.chisq is the same as those of the function chisq.test. Part of the values are listed below:

statistic the value the chi-squared test statistic.
parameter the degrees of freedom of the approximate chi-squared distribution of the test statistic, 'NA' if the p-value is computed by Monte Carlo simulation.
p.value the p-value for the test.

Author(s)

Gregory R. Warnes gregory.r.warnes@pfizer.com and Nitin Jain nitin.jain@pfizer.com

See Also

HWE.exact

Examples

library(GeneticsBase)
data(CAMP)

HWE.chisq(CAMP, marker="m654")


[Package GeneticsBase version 1.2.0 Index]