permutations {globaltest} | R Documentation |
Produces a histogram for visualization of the permutations
used in globaltest
.
permutations(gt, geneset = NULL, nperm = 10^4)
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). |
nperm |
The number of permutations to be used. |
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.
NULL
(no output except the plot).
Permutations does not work if the adjusted version of globaltest was used.
Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting
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.
globaltest
, sampleplot
,
geneplot
.
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) }