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Last data update: 2014.03.03

R: Exact test for Hardy-Weinberg equilibrium

HWExactPrevious

R Documentation

Exact test for Hardy-Weinberg equilibrium

Description

HWExactPrevious performs an exact test for Hardy-Weinberg equilibrium

Usage

HWExactPrevious(X, alternative = "two.sided", pvaluetype = "selome",
x.linked = FALSE, verbose = FALSE)

Arguments

`X`	vector with the genotype counts AA, AB, BB
`alternative`	`two.sided` (default) will perform a two-sided test where both an excess and a dearth of heterozygotes count as evidence against HWE. `less` is a one-sided test where only dearth of heterozygotes counts a evidence against HWE, `greater` is a one-sided test where only excess of heterozygotes counts as evidence against HWE.
`pvaluetype`	if `pvaluetype` is set to `dost` then the p-value of a two-sided test is computed as twice the tail area of a one-sided test. When set to `selome`, the p-value is computed as the sum of the probabilities of all samples less or equally likely as the current sample. When set to `midp`, the p-value is computed as half the probability of the current sample + the probabilities of all samples that are more extreme.
`x.linked`	`x.linked=FALSE` indicates the marker is autosomal (default), and `x.linked=TRUE` indicates it resides on the X-chromosome.
`verbose`	print results or not.

Details

HWExactPrevious uses the recursion equations described by Wigginton et. al.

For large samples, HWExactPrevious may give the error message: "evaluation nested too deeply: infinite recursion". This can usually be resolved by increasing R's limit on nested expressions with options(expressions=10000) or a higher limit. With higher limits, the error message "protect(): protection stack overflow" can occur. This error can usually be resolved by increasing R's protection stack with the command line option --max-ppsize 100000 or higer values. However, with such large samples the exact test will give virtually the same result as a chi-square test, and it may be easier to use HWChisq in these circumstances.

Value

`pval`	p-value of the exact test
`prob`	probabilities of all possible samples with the same sample size and minor allele count
`pofthesample`	probability of the observed sample

Author(s)

Jan Graffelman (jan.graffelman@upc.edu)

References

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

Wigginton, J.E., Cutler, D.J. and Abecasis, G.R. (2005) A note on exact tests of Hardy-Weinberg equilibrium, American Journal of Human Genetics (76) pp. 887-893.

Examples

#
# Example autosomal marker
#
x <- c(298,489,213)
names(x) <- c("MM","MN","NN")
HW.test <- HWExactPrevious(x,verbose=TRUE)
#
# Example x-linked marker
#
rs5968922  <- c(A=392, B=212, AA=275, AB=296, BB=80 )
HWExactPrevious(rs5968922,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.

R is a collaborative project with many contributors.
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/HWExactPrevious.Rd_%03d_medium.png", width=480, height=480)
> ### Name: HWExactPrevious
> ### Title: Exact test for Hardy-Weinberg equilibrium
> ### Aliases: HWExactPrevious
> ### Keywords: htest
> 
> ### ** Examples
> 
> #
> # Example autosomal marker
> #
> x <- c(298,489,213)
> names(x) <- c("MM","MN","NN")
> HW.test <- HWExactPrevious(x,verbose=TRUE)
Haldane's Exact test for Hardy-Weinberg equilibrium
using SELOME p-value
sample counts: nMM =  298 nMN =  489 nNN =  213 
H0: HWE (D==0), H1: D <> 0 
D =  -3.69375 p =  0.6556635 
> #
> # Example x-linked marker
> #
> rs5968922  <- c(A=392, B=212, AA=275, AB=296, BB=80 )
> HWExactPrevious(rs5968922,x.linked=TRUE,verbose=TRUE) 
Graffelman-Weir exact test for Hardy-Weinberg equilibrium on the X-chromosome
using SELOME p-value
Sample probability 0.002818315 p =  1 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>