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 larger standardized test statistic
(Q - EQ) / sd(Q) 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
Jelle J. Goeman, Jan Oosting, Anne-Marie Cleton-Jansen, Jakob, K. Anninga, Hans C. van Houwelingen (2005) Testing association of a pathway with survival. Bioinformatics 21, 1950-1957. See also the vignette Globaltest.pdf that comes with this package.
globaltest
, permutations
,
sampleplot
, geneplot
.
# Breast cancer data (ExpressionSet) from the Netherlands Cancer # Institute with annotation: data(vandeVijver) data(annotation.vandeVijver) gt <- globaltest(vandeVijver, "StGallen", annotation.vandeVijver) sampling(gt, ndraws=100)