permutations {globaltest}R Documentation

Permutations Plot for Global Test

Description

Produces a histogram for visualization of the permutations used in globaltest.

Usage

permutations(gt, geneset = NULL, nperm = 10^4)

Arguments

gt The output of a call to globaltest.
geneset The name or number of the geneset to be plotted (only necessary if multiple genesets were tested).
nperm The number of permutations to be used.

Details

Produces a histogram of the value of the test statistic calculated for permutations of the clinical outcome, compared with the test statistic for the true clinical outcome.

Value

NULL (no output except the plot).

Note

Permutations does not work if the adjusted version of globaltest was used.

Author(s)

Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting

References

J. J. Goeman, S. A. van de Geer, F. de Kort and J. C. van Houwelingen, 2004, A global test for groups of genes: testing association with a clinical outcome, Bioinformatics 20 (1) 93–99. See also the How To Globaltest.pdf included with this package.

See Also

globaltest, sampleplot, geneplot.

Examples

if (interactive()) {
    data(exampleX)      # Expression data (40 samples; 1000 genes)
    data(exampleY)      # Clinical outcome for the 40 samples
    pathway <- 1:25     # A pathway contains genes 1 to 25
    gt <- globaltest(exampleX, exampleY, test.genes = pathway, 
                                                permutation = TRUE)
    gt
    permutations(gt)
}

[Package globaltest version 2.1.6 Index]