HardyWeinberg: HWChisqStats – R documentation

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HWChisqStats

Fast computation of chi-square statistics for Hardy-Weinberg equilibrium

Description

HWChisqStats is a function for the fast computation of chi-square statistics (or the corresponding p-values) for a large set of bi-allelic markers (typically SNPs).

Usage

HWChisqStats(X, x.linked = FALSE, pvalues = FALSE)

Arguments

`X`	A matrix with genotype counts, one row per marker. `X` should have 5 columns for an X-chromosomal data set and 3 columns for an autosomal data set.
`x.linked`	Logical indicating whether the markers are autosomal (`x.linked=FALSE`) or X-chromosomal (`x.linked=TRUE`).
`pvalues`	Logical indicated whether chi-square statistics should be returned (`pvalues=FALSE`) or whether p-values should be returned (`pvalues=TRUE`).

Details

Matrix X should strictly comply with the following format. For an autosomal dataset is should contain the 3 genotype counts in order (AA,AB,BB). For an X-chromosomal dataset it should contain the 5 genotype counts in order (A,B,AA,AB,BB) where A and B are the male counts and AA, AB and BB the female counts.

This function was written for speed improvement, and should be much faster than looping over the rows of X with HWChisq. There is no error checking on the supplied data matrix.

Value

A vector of chi-square statistics

Author(s)

Jan Graffelman jan.graffelman@upc.edu

References

Graffelman, J. and Weir, B.S. (2016) Testing for Hardy-Weinberg equilibrium at 2 bi-allelic genetic markers on the X chromosome.

Examples

#
# Autosomal example
#
set.seed(123)
X <- HWData(1000,100)
monom <- (X[,2]==0 & X[,1]==0) | (X[,2]==0 & X[,3]==0)
X <- X[!monom,] # exclude monomorphics
Chisq.stats <- HWChisqStats(X,x.linked=FALSE,pvalues=FALSE)
Chisq.pvals <- HWChisqStats(X,x.linked=FALSE,pvalues=TRUE)
#
# X-chromosomal example
#
X <- HWData(1000,100,n.males=50,nA=75,x.linked=TRUE)
Chisq.stats <- HWChisqStats(X,x.linked=TRUE,pvalues=FALSE)
Chisq.pvals <- HWChisqStats(X,x.linked=TRUE,pvalues=TRUE)

HardyWeinberg

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

v1.7.2

GPL (>= 2)

Authors

Jan Graffelman [aut, cre], Christopher Chang [ctb], Xavi Puig [ctb], Jan Wigginton [ctb], Leonardo Ortoleva [ctb], William R. Engels [ctb]

Initial release

2021-04-28