HardyWeinberg (version 1.7.8)

HWExactStats: Computation of Exact p-values for Hardy-Weinberg equilibrium for sets of SNPs

Description

HWExactStats is a function for the computation of Exact p-values for a large set of bi-allelic markers (typically SNPs).

Usage

HWExactStats(X, x.linked = FALSE, plinkcode = TRUE, midp = FALSE,...)

Value

A vector of p-values

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).

plinkcode

Logical indicating whether to use faster C++ code from the PLINK software.

midp

Logical indicating whether to use the mid p-value for the C++ code or not

...

extra arguments that are passed on to HWExact

Author

Jan Graffelman (R code) and Christopher Chang (C++ code)

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.

Argument plinkcode=TRUE (the default) will use C++ code for faster calculation (functions SNPHWE2 and SNPHWEX) with larger datasets. The C++ code was generously shared by Christopher Chang, and the same code is used in the program PLINK (2.0).

References

Graffelman, J. and Weir, B.S. (2016) Testing for Hardy-Weinberg equilibrium at bi-allelic genetic markers on the X chromosome. Heredity 116(6) pp. 558--568. tools:::Rd_expr_doi("10.1038/hdy.2016.20")

Purcell et al. (2007) PLINK: A Toolset for Whole-Genome Association and Population-Based Linkage Analysis. American Journal of Human Genetics 81(3) pp. 559--575.

See Also

HWExact

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
Exact.pvalues <- HWExactStats(X,x.linked=FALSE)
#
# X-chromosomal example
#
X <- HWData(1000,100,n.males=50,nA=75,x.linked=TRUE)
Exact.pvalues <- HWExactStats(X,x.linked=TRUE)