permutations {globaltest}R Documentation

Histogram for Global Test result

Description

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

Usage

permutations(testresult)

Arguments

testresult The output of a call to globaltest.

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).

Note

Only works if the option permutation = TRUE was chosen when calling globaltest.

Author(s)

Jelle Goeman: j.j.goeman@lumc.nl

References

J. J. Goeman, S.A. van de Geer, F. de Kort and J. C. van Houwelingen, A global test for association of a group of genes with a clinical outcome, Technical Report MI 2003-03, Mathematical Institute, Leiden University. Available from http://www.math.leidenuniv.nl/~jgoeman.

See Also

globaltest, checkerboard, geneplot, regressionplot.

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 Contents]