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

In OCplus: Operating characteristics plus sample size and local fdr for microarray experiments

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

## S3 method for class 'FDR.result'
plot(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

Author(s)

A. Ploner

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)

OCplus documentation built on Nov. 8, 2020, 5:20 p.m.