permutations {globaltest}R Documentation

Permutations version of the Global Test

Description

Produces permutations of the globaltest test statistic and uses these to recalculate the p-value.

Usage

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

Arguments

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

Details

A permutation p-value is calculated by comparing the value of the test statistic for random permutations of the clinical outcome to the value of the test statistic for the true clinical outcome. The permuted test statistics are stored for later visualisation using hist.

Value

An object of class gt.result.

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

    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)
    gt

    perm.gt <- permutations(gt)
    perm.gt

    if (interactive()) {
      hist(perm.gt)
    }

[Package globaltest version 3.2.0 Index]