geneplot {globaltest}R Documentation

Gene Plot for Global Test

Description

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

Usage

geneplot(gt, geneset, genesubset, scale = FALSE, 
            drawlabels = TRUE, labelsize = 0.6, ...)

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).
genesubset A vector of names or numbers of genes to be plotted (default: plot all genes)
scale Logical: should the bars be scaled to unit standard deviation?
drawlabels Logical value to control drawing of gene ids (rownames) on the x-axis of the plot.
labelsize Relative size of the labels on the x-axis. If it is NULL , the current value for par("cex.axis") is used
... Any extra arguments will be forwarded to the plotting function.

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 test statistic Q is the average of the bars of the genes. The reference line shows the expected influence if the gene was not associated with the outcome. The marks on the bars show the standard deviation of the bar under the null hypothesis. The color of the bar indicates positive or negative correlation of the gene with the clinical outcome, to distinguish between up and downregulation.

The bottom margin is adjusted to allow enough space for the longest gene id to draw under the axis.

Value

An object of type gt.barplot.

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.

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
    
    if (interactive()){ 
      geneplot(gt)
    }

[Package globaltest version 3.2.0 Index]