permutations {globaltest} | R Documentation |
Produces permutations of the globaltest
test
statistic and uses these to recalculate the p-value.
permutations(gt, geneset, nperm = 10^4)
gt |
The output of a call to globaltest . |
geneset |
The name or number of the geneset(s) to be used (only necessary if multiple genesets were tested). |
nperm |
The number of permutations to be used. |
A permutation p-value is calculated by comparing
the value of the test statistic for random permutations of the clinical outcome
to the value of the test statistic for the true clinical outcome.
The permuted test statistics are stored for later visualisation using
hist
.
An object of class
gt.result
.
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
.
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 perm.gt <- permutations(gt) perm.gt if (interactive()) { hist(perm.gt) }