OCplus (version 1.46.0)

plot.FDR.result: Plot the empirical FDR as a function of the cutoff level

Description

Plots the output from EOC. The resulting graph is the empirical counterpart to those produced by TOC, i.e. the estimated FDR as a function of the cutoff-level on the t-statistic.

Usage

plot.FDR.result(x, add=FALSE, sensitivity.show = TRUE, legend.show = FALSE,  xlim, ylim = c(0, 1), xlab, ylab, main, ...)

Arguments

x

an object created by EOC

add

logical value indicating whether to add to an existing plot or start a new one

sensitivity.show

logical value indicating whether to show the classical sensitivity for testing one hypothesis as a function of the cutoff level.

legend.show

logical value indicating whether to add a legend to the plot

xlim, ylim

limits for the horizontal and vertical axis

xlab, ylab

axis labels

main

plot title

...

the usual graphical parameters, passed to plot

See Also

EOC

Examples

# We simulate a small example with 5 percent regulated genes and
# a rather large effect size
set.seed(2003)
xdat = matrix(rnorm(50000), nrow=1000)
xdat[1:25, 1:25] = xdat[1:25, 1:25] - 2
xdat[26:50, 1:25] = xdat[26:50, 1:25] + 2
grp = rep(c("Sample A","Sample B"), c(25,25))

# Compute the EOC without plotting
ret = EOC(xdat, grp, plot=FALSE) 

# Some possible arrangements
par(mfrow=c(2,2))
plot(ret)
plot(ret, legend=TRUE)
plot(ret, sensitivity=FALSE)