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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(OCplus)
Loading required package: akima
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/OCplus/plot.FDR.result.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.FDR.result
> ### Title: Plot the empirical FDR as a function of the cutoff level
> ### Aliases: plot.FDR.result
> ### Keywords: hplot aplot
> 
> ### ** 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)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>