permutations {globaltest} | R Documentation |
Produces a histogram for visualization of the permutations
used in globaltest
.
permutations(testresult)
testresult |
The output of a call to globaltest . |
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).
Only works if the option permutation = TRUE
was
chosen when calling globaltest
.
Jelle Goeman: j.j.goeman@lumc.nl
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.
globaltest
, checkerboard
,
geneplot
, regressionplot
.
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) }