Chi square tests for Hardy Weinberg equilibrium

Description

HWChisq performs the chi-square test for Hardy-Weinberg equilibrium both for autosomal and X-chromosomal markers.

Usage

HWChisq(X, cc = 0.5, verbose = TRUE, x.linked = FALSE, phifixed = NULL) 

Arguments

Details

HWChisq does a chi-square test for Hardy-Weinberg equilibrium, and by default applies a continuity correction. For extreme allele frequencies, the continuity correction can lead to excessive type 1 error rates, and is better turned off in that case. The continuity correction can be turned off by specifying cc=0.

HWChisq can do the chi-square test for both autosomal and X-chrosomal markers. By setting x.linked = TRUE the marker will be assumed to be on the X-chromosome, and the count vector supplied should have 5 elements instead of 3 elements for an autosomal marker. For X-chromsomal markers argument phifixed is in general best left to its default value (NULL). Only in specific situations where the theoretical population sex ratio is known (e.g. in simulation studies where a universe with known gender ratio is sampled) phifixed could be set to the theoretical ratio of interest.

When alternative is set to less, a one-sided test for against a negative inbreeding coefficient (heterozygote excess) is performed. When alternative is set to greater a one-sided test for against a positive inbreeding coefficient (lack of heterozygotes) is performed.

Value

HWChisq returns a list with the components:

Author(s)

Jan Graffelman jan.graffelman@upc.edu

References

Weir, B.S. (1996) Genetic data analysis II. Sinauer Associates, Massachusetts. See Chapter3.

See Also

HWLratio, HWChisqStats

Examples

#
# Test for an autosomal blood group marker
#
x <- c(MM=298,MN=489,NN=213)
HW.test <- HWChisq(x,verbose=TRUE)
#
# Same test without continuity correction
#
HW.test <- HWChisq(x,cc=0,verbose=TRUE)
#
# Test for an X-chromsomal SNP.
#
rs5968922 <-  c(A=392, B=212, AA=275, AB=296, BB=80)
HW.test <- HWChisq(rs5968922,cc=0,x.linked=TRUE,verbose=TRUE)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(HardyWeinberg)
Loading required package: mice
Loading required package: Rcpp
mice 2.25 2015-11-09
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HardyWeinberg/HWChisq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: HWChisq
> ### Title: Chi square tests for Hardy Weinberg equilibrium
> ### Aliases: HWChisq
> ### Keywords: htest
> 
> ### ** Examples
> 
> #
> # Test for an autosomal blood group marker
> #
> x <- c(MM=298,MN=489,NN=213)
> HW.test <- HWChisq(x,verbose=TRUE)
Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.1789563 DF =  1 p-value =  0.6722717 D =  -3.69375 f =  0.01488253 
> #
> # Same test without continuity correction
> #
> HW.test <- HWChisq(x,cc=0,verbose=TRUE)
Chi-square test for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.2214896 DF =  1 p-value =  0.6379073 D =  -3.69375 f =  0.01488253 
> #
> # Test for an X-chromsomal SNP.
> #
> rs5968922 <-  c(A=392, B=212, AA=275, AB=296, BB=80)
> HW.test <- HWChisq(rs5968922,cc=0,x.linked=TRUE,verbose=TRUE)
Chi-square test for Hardy-Weinberg equilibrium (X-chromosomal)
Chi2 =  0.00170001 DF = 2 p-value =  0.9991504 D =  NA f =  0.0009953963 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>