getSigGroups: Interfaces for running the enrichment tests

In hxin/topOnto: ontology enrichment analysis

Description

These function are used for dispatching the specific algorithm for a given topONTdata object and a test statistic.

Usage

getSigGroups(object, test.stat, ...)
runTest(object, algorithm, statistic, ...)
whichAlgorithms()
whichTests()

Arguments

object	An object of class topONTdata This object contains all data necessary for runnig the test.
test.stat	An object of class groupStats. This object defines the test statistic.
algorithm	Character string specifing which algorithm to use.
statistic	Character string specifing which test to use.
...	Other parameters. In the case of runTest they are used for defining the test statistic

Details

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.

...

Value

An object of class topGOresult

Author(s)

Adrian Alexa

See Also

topONTdata-class, groupStats-class, topGOresult-class

Examples

## load a sample topONTdata object
data(ONTdata)
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")

hxin/topOnto documentation built on May 17, 2019, 9:15 p.m.