evalClusterHyper {goCluster} | R Documentation

## Evaluates a clustering result with regard to an enrichment of annotation terms in specific clusters.

### Description

The function `evalClusterHyper` moves through a tree of gene groups and calls the function `evalAnnosetHyper` for each of them. This second function employs the hypergeometric distributon to calculate a p-value for each of the annotation terms that is annotated to the genes in the group.

### Usage

    evalClusterHyper(X, uniqueid, Annoset)
    evalAnnosetHyper(Selection, uniqueid, Annoset)

### Arguments

`X` | The tree (list of lists) of clusters.
`Annoset` | This is a list with each element holding a different annotation dataset. Each of this dataset is composed of two columns with the first column matching the ids of the genes given in the clusters, while the second column holds the corresponding annotation terms.
`uniqueid` | The unique id of the elements in the dataset.
`Selection` | A list of genes that comprise one cluster. The ids given here have to match the ids from the first column of the annotation dataterms.

### Details

This class uses a "tree" (list of lists) of gene groups and analyzes the frequency of associated annotation terms within these groups using the hypergeometric distribution. For each group the unique annotation terms will be extracted and all genes matching these terms are selected as a reference set. The algorithm will then use the hypergeometric distribution to determine for each available annotation term in that group whether the genes in the group that match this term are enriched in this

### Value

`pvalues` | Description of 'comp1'
`selectedPerAnnotation` | A vector that holds the number of times the annotation was found in the given selection.
`elementsPerAnnotation` | A vector that holds the number of times the annotation was found over all elements.
`selectedTotal` | Total number of annotation terms in the given selection.
`elementsTotal` | Total number of annotation terms over all elements.

### Author(s)

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

### See Also

`clusterStatisticHyper-class`

### Examples

    ## FIXME

[Package goCluster version 1.0.0 Index]