snpgdsHWE: Statistical test of Hardy-Weinberg Equilibrium

In zhengxwen/SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Statistical test of Hardy-Weinberg Equilibrium

Description

Calculate the p-values for the exact SNP test of Hardy-Weinberg Equilibrium.

Usage

snpgdsHWE(gdsobj, sample.id=NULL, snp.id=NULL, with.id=FALSE)

Arguments

gdsobj	an object of class SNPGDSFileClass, a SNP GDS file
sample.id	a vector of sample id specifying selected samples; if NULL, all samples will be used
snp.id	a vector of snp id specifying selected SNPs; if NULL, all SNPs will be used
with.id	if TRUE, the returned value with sample and SNP IDs

Value

If with.id=FALSE, return a vector of numeric values (p-value); otherwise, return a list with three components "pvalue", "sample.id" and "snp.id".

Author(s)

Xiuwen Zheng, Janis E. Wigginton

References

Wigginton, J. E., Cutler, D. J. & Abecasis, G. R. A note on exact tests of Hardy-Weinberg equilibrium. Am. J. Hum. Genet. 76, 887-93 (2005).

See Also

snpgdsSNPRateFreq

Examples

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())

# Japanese samples
sample.id <- read.gdsn(index.gdsn(genofile, "sample.id"))
pop <- read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))
(samp.sel <- sample.id[pop=="JPT"])
samp.sel <- samp.sel[nchar(samp.sel) == 7]

# chromosome 1
snp.id <- snpgdsSelectSNP(genofile, sample.id=samp.sel, autosome.only=1L)

# HWE test
p <- snpgdsHWE(genofile, sample.id=samp.sel, snp.id=snp.id)
summary(p)

# QQ plot
plot(-log10((1:length(p))/length(p)), -log10(p[order(p)]),
	xlab="-log10(expected P)", ylab="-log10(observed P)", main="QQ plot")
abline(a=0, b=1, col="blue")

# close the genotype file
snpgdsClose(genofile)

zhengxwen/SNPRelate documentation built on Nov. 19, 2024, 1:02 p.m.