sampling {globaltest} | R Documentation |
For every pathway in a result of globaltest
,
calculates how many randomly drawn groups of genes of the same size have a
smaller or equal p-value.
sampling(gt, geneset, ndraws = 10^3)
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). |
ndraws |
The number of random pathways to be used. |
For every pathway in gt[geneset]
, a number ndraws
random 'pathways' is selected by randomly sampling sets of genes of the same
size as the tested pathway. A 'comparative p-value' is calculated by counting
what proportion of the random pathways has a smaller or equal p-value than
the tested pathway.
An object of class
gt.result
.
The function sampling
cannot be applied to a
gt.result
object resulting from a call to
permutations
.
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
, permutations
,
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 <- sampling(globaltest(exampleX, exampleY, test.genes = pathway)) gt