Description Usage Arguments Value Author(s) References See Also Examples
Calculate the p-values for the exact SNP test of Hardy-Weinberg Equilibrium.
1 |
gdsobj |
an object of class |
sample.id |
a vector of sample id specifying selected samples;
if |
snp.id |
a vector of snp id specifying selected SNPs;
if |
with.id |
if |
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".
Xiuwen Zheng, Janis E. Wigginton
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).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | # 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)
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