checkerboard {globaltest}R Documentation

Checkerboard plot for Global Test result

Description

Produces a plot to visualize the test result produced by globaltest, by showing the association between pairs of samples.

Usage

checkerboard(testresult, sort = TRUE)

Arguments

testresult The output of a call to globaltest.
sort A logical flag to indicate whether the samples should be sorted by the clinical outcome to give a clearer picture.

Details

The checkerboard shows the pairs of samples which have high covariance in white and the pairs with low covariance in black. This can be used to visualize the data and to search for outlying arrays.

Value

A matrix giving the old and the new sample numbers.

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, geneplot, 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
    checkerboard(gt)
}

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