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 using permutations of the clinical outcome to
the value of the test statistic for the true clinical outcome. If
the number of possible permutations is smaller than the value of
nperm
, all possible permutations are used, otherwise
nperm
random permutations. 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
For references, type: citation("globaltest"). See also the vignette GlobalTest.pdf included with this package.
globaltest
, sampleplot
,
geneplot
.
# Breast cancer data (ExpressionSet) from the Netherlands Cancer # Institute with annotation: data(vandeVijver) data(annotation.vandeVijver) aPathway <- annotation.vandeVijver[1] gt <- globaltest(vandeVijver, "StGallen", aPathway) perm.gt <- permutations(gt) if (interactive()) { hist(perm.gt) }