regressionplot {globaltest}R Documentation

Regression Plot for Global Test

Description

Produces a plot which can be used to visualize the effect of specific samples on the test result produced by globaltest.

Usage

regressionplot(gt, geneset, sampleid, ...)

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).
sampleid An optional vector of names or numbers of the samples of interest.
... Any extra arguments will be forwarded to the plotting function.

Details

The regressionplot plots, for all pairs of samples, the covariance between the expression patterns against the covariance between their clinical outcomes. Each point in the plot therefore represents a pair of samples. A regression line is fitted through the samples, which visualizes the test result of the function globaltest. A steeply increasing slope indicates a high (possibly significant) value of the test statistic.

An optional argument sampleid can be supplied, giving sample numbers of possibly outlying arrays. In this case, all pairs of arrays involving one of the arrays in sampleid is marked as a red cross, while the other pairs are marked as a blue dot. The blue line which is fitted through all points can now be compared to a red dotted line which is fitted though only the red crosses.

Value

NULL (no output).

Note

Regressionplot 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)
    gt
    regressionplot(gt)
    regressionplot(gt, sampleid = 40)
}

[Package globaltest version 3.2.0 Index]