HWQqplot {HardyWeinberg}

A Q-Q plot for Hardy-Weinberg equilibrium

Description

HWQqplot creates a Q-Q plot for the p-values obtained in an Exact test for Hardy-Weinberg equilibrium. Empirical p-values are plotted against multiple simulated quantiles of the theoretical p-value distribution.

Usage

HWQqplot(X, nsim = 100, fit = "curve", logplot = FALSE,
main = "Q-Q plot for HWE", mm = NULL, pvaluetype = "selome", ...)

Arguments

X

Data matrix with genotype counts, one row for each sample, 3 columns

nsim

Number of samples drawn from the null distribution (100 by default)

fit

If fit is set to "line" straight lines will be fitted to the simulated samples, if set to "curve", ascending curves will be shown.

logplot

If logplot is set to true, then the log10 of the p-values will be used in the plot. If not, untransformed p-values will be used.

main

Title for the plot

mm

Maximal value for x and y axis in the plot

pvaluetype

Type of p-value to be used in an exact test. Can be "selome" (default), "midp" or "dost".

...

Any additional arguments for the plot instruction

Details

HWQqplot constructs a Q-Q plot of the p-values of an exact test for Hardy-Weinberg equilibrium. Under the null, this p-value is not uniform. HWQqplot samples from the theoretical null distribution, taking into account that markers may vary in allele frequency and in sample size (due to missing values). For each simulated sample a grey curve or line is shown. A green reference line with intercept 0 and slope 1 is also shown in the plot.

Value

NULL

Author(s)

Jan Graffelman [e-mail]

References

Rohlfs, R.V. and Weir, B.S. (2008) Distributions of Hardy-Weinberg equilibrium test statistics. Genetics 180, pp. 1609-1616.

See Also

HWTernaryPlot, HWExact, qqplot

Examples

## Not run: 
set.seed(1234)
n <- 200 # sample size
m <- 100 # number of markers
X <- HWData(n,m)
HWQqplot(X,logplot=TRUE,pvaluetype="selome",main="Q-Q Plot for HWE")

## End(Not run)