plot.FDR.result {OCplus} | R Documentation

## 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

    ## 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)

[Package OCplus version 1.66.0 Index]