selectStats {goCluster} | R Documentation

## Selects relevant annotation terms

### Description

This function removes all annotation terms with a p-value higher than the given threshold from the given tree.

### Usage

    selectStats(X, threshold)

### Arguments

`X` | The tree of annotation terms as retrieved by the statistical analysis function (e.g. evalClusterHyper)
`threshold` | The selection threshold for the p-values.

### Details

The function will walk through all nodes of the tree specified as X and removes all annotation terms with a p-value lower than the given threshold. The resulting tree will have the same structure as before but it can contain nodes that are empty. This function does perform no correction for multiple testing whatsoever and should be used with caution.

### Value

A reduced tree with annotation elements having a "significant" p-value.

### Author(s)

Gunnar Wrobel, work@gunnarwrobel.de, http://www.gunnarwrobel.de.

### See Also

`clusterSignifBase-class`

### Examples

    set.seed(1000)

    data(benomylsetupsmall)

    a <- new("goCluster")

    execute(a) <- benomylsetupsmall

    ## The statistics are saved in the "statset" slot of
    ## the "stat" object that is itself a child of the "sign"
    ## object of a "goCluster" object
    ## We select all items with a p-value below 0.05 here.
    selectStats(a@sign@stat@statset,0.05)

[Package goCluster version 1.4.0 Index]