QQperm (version 1.0.1)

qqplot: QQ plot of observed P-values vs expected P-values, using the empirical (permutation-based) expected p-value distribution. This empirical-based expected p-value distribution no longer depends on an assumption that the Fisher's Exact two-tailed p-values are uniformly distributed under the null. For a given matrix, the permutation-based expected distribution is plotted relative to the observed order statistic to get the permutation-based QQ plot.

Description

QQ plot of observed P-values vs expected P-values, using the empirical (permutation-based) expected p-value distribution. This empirical-based expected p-value distribution no longer depends on an assumption that the Fisher's Exact two-tailed p-values are uniformly distributed under the null. For a given matrix, the permutation-based expected distribution is plotted relative to the observed order statistic to get the permutation-based QQ plot.

Usage

qqplot(P.perm, P.observed, adjust.xy = TRUE, ...)

Arguments

P.perm

Expected P-values from NULL distribution, which is generated through permutation in our example.

P.observed

Observed P-values from true case/control assignment.

adjust.xy

An option to have the x-axis and y-axis adjusted based on their own range in the plot.

...

Additional arguments passed to the plot function.

Value

None.

Examples

library(QQperm)
data("example.Ps")

#print output to pdf file only if not running in interactive mode
if (!interactive()) {
 pdf("qqplot.pdf")
}

qqplot(example.Ps$perm, example.Ps$observed)

if (!interactive()) {
 dev.off()
}