getSigGroups {topGO} | R Documentation |
These function are used for dispatching the specific algorithm for
a given topGOdata
object and a test statistic.
getSigGroups(object, test.stat, ...) runTest(object, algorithm, statistic, ...) whichAlgorithms() whichTests()
object |
An object of class |
test.stat |
An object of class |
algorithm |
Character string specifing which algorithm to use. |
statistic |
Character string specifing which test to use. |
... |
Other parameters. In the case of |
The runTest
function can be used only with a predefined set of
test statistics and algorithms. The algorithms and the statistical
tests which are accessible via the runTest
function are shown
by the whichAlgorithms()
and whichTests()
functions.
The runTest function is a warping of the getSigGroups
and the
initialisation of a groupStats
object functions.
...
An object of class topGOresult
.
Adrian Alexa
topGOdata-class
,
groupStats-class
,
topGOresult-class
## load a sample topGOdata object data(GOdata) GOdata ############################## ## getSigGroups interface ############################## ## define a test statistic test.stat <- new("classicCount", testStatistic = GOFisherTest, name = "Fisher test") ## perform the test resultFis <- getSigGroups(GOdata, test.stat) resultFis ############################## ## runTest interface ############################## ## Enrichment analysis by using the "classic" method and Fisher's exact test resultFis <- runTest(GOdata, algorithm = "classic", statistic = "fisher") resultFis ## weight01 is the default algorithm weight01.fisher <- runTest(GOdata, statistic = "fisher") weight01.fisher ## not all combinations are possible! # weight.ks <- runTest(GOdata, algorithm = "weight", statistic = "t")