prepareGOannotation {goCluster} | R Documentation

## A function to prepare the gene ontology annotation for subsequent statistical analysis

### Description

This function builds an association table between a given list of genes and their corresponding gene ontology annotations.

### Usage

    prepareGOannotation(uniqueID,
    annBuilderPkg,
    ontologies = ONTOLOGIES,
    evidence = EVIDENCECODES,
    trueID = NULL)

### Arguments

`uniqueID` | The unique ID that should be associated with the gene ontology annotation.
`annBuilderPkg` | The AnnBuilder package that provides the basis for retrieving the annotation information.
`ontologies` | The ontologies that should be used. This has to be a character vector that contains one or more of the strings "MF", "BP", and/or "CC".
`evidence` | This character vector should contain the abbreviations for acceptable evidence codes. Please see the variable EVIDENCECODES for possible choices. The complete vector with all evidence codes is the default for the function.
`trueID` | The true ID specifies the type of ID that the gene ontology information has been linked to (e.g. Locus Link). If this ID differs from the the type of `uniqueID` this has to be specified so that the IDs are converted accordingly. The option needs to match the name of the AnnBuilder package environment (without the prefix) that provides the conversion information.

### Details

The gene ontology is organized as a hierarchical tree of terms with a parent-child relationship. By associating a gene with a term of this ontology the gene is implicitely linked with all parents of the term. In order to render the annotation of two gene lists comparable it is important to take this relationship into account.

The `prepareGOannotation` function assembles a complete list of gene <-> ontology associations based on the gene ontology annotation. Duplicate genes are removed from the resulting table. This removal should be based on the identifiers the gene ontology information is linked to (e.g. Lokus Link) and it is possible to specify this central ID by setting the `trueid` option.

### Value

A composite list of the (possibly converted) unique ID and the association table.

`annotations` | The association table linking the genes with gene ontology terms. Each gene can be linked to multiple GO entries and vice versa.
`uniqueid` | Either a copy of the original unique identifiers or a converted copy that matches the original vector in length but specifies the new gene ID for each gene.

### Author(s)

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

### See Also

`clusterAnnotationGO-abp-class`

### Examples

    prepareGOannotation(c("YGL213C", "YGL215W", "YGL216W", "YGL218W",
    "YGL219C", "YGL220W", "YGL221C", "YGL222C", "YGL223C", "YGL224C",
    "YGL225W"), "YEAST")

[Package goCluster version 1.6.0 Index]