geneplot {globaltest}R Documentation

Geneplot for Global Test result

Description

Produces a plot to show the influence of individual genes on the test result produced by globaltest.

Usage

geneplot(testresult)

Arguments

testresult The output of a call to globaltest.

Details

The geneplot shows a bar an a reference line for each gene. The bar shows the influence of each gene on the test result; the reference line shows the expected influence if the gene was not associated with the outcome. The color of the bar indicates positive or negative correlation of the gene with the clinical outcome, to distinguish between up and downregulation.

Value

If gene names were supplied in the call to globaltest, geneplot returns a data.frame referring the gene names to the gene numbers appearing in the plot. Otherwise NULL.

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, regressionplot, checkerboard, permutations.

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)
    gt
        geneplot(gt)
}

[Package Contents]