getSigGroups {topGO} | R Documentation

## Interfaces for running the enrichment tests

### Description

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

### Usage

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

### Arguments

`object` | An object of class `topGOdata` 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

`topGOdata-class`, `groupStats-class`, `topGOresult-class`

### Examples

    ## 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")

[Package topGO version 2.39.1 Index]