GOEnrichment {tRanslatome} | R Documentation

## GOEnrichmentHelpfile

### Description

GOEnrichment is a function which, given as input an object of class `DEGs`, identifies overrepresented GO terms among differentially expressed genes. The analysis can be applied to all the GO ontologies or restricted to GO terms specifically belonging to one ontology: molecular function, cellular component or biological process. Moreover the function can identify enriched GO terms for separate classes of genes of interest: only up-regulated genes, only down-regulated genes or both of them together. The output of the function is an object of class `GOsets`, containing the results of the enrichment analysis.

### Usage

    GOEnrichment(object, ontology="all", classOfDEGs="both",
        test.method="classic", test.threshold = 0.05, mult.cor=TRUE)

### Arguments

`object` | an object of class `DEGs`
`ontology` | a character string specifying the GO ontology of interest: `CC` for Cellular Component, `BP` for Biological Process, `MF` for Molecular Function or `all` for all the three ontologies. The default is set to `all`.
`classOfDEGs` | a character string specifying the class of genes for which we want to detect enriched GO terms: `up` for considering only up-regulated genes, `down` for considering only down-regulated genes, `both` for considering all DEGs, independently from the direction of their changes. The default is set to `both`.
`test.method` | a character string specifying the statistical method to calculate the enrichment. By default it is set to `classic` (enrichment is measured with the classic Fisher exact test), but it can also be set to `elim`, `weight`, `weight01` or `parentchild`. All these methods are implemented in the `topGO` Bioconductor package
`test.threshold` | a numeric value specifying the significance threshold upon which the GO terms are considered significantly over-represented. By default it is se to `0.05`.
`mult.cor` | a boolean variable specifying whether the significance threshold is applied to the multiple test corrected or to the original p-values obtained from the selected enrichment method. By default it is set to `TRUE`.

### Value

An object of class `GOsets`

### Author(s)

Toma Tebaldi, Erik Dassi, Galena Kostoska

### References

Ashburner M et al(2000). Gene ontology: tool for the unification of biology. Nat. Genet. May 2000;25(1):25-9.

Alexa A, Rahnenfuhrer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating go graph structure. Bioinformatics 2006, 22(13):1600-7

### See Also

`GOComparison` `GOsets` `GOsims`

### Examples

    data(tRanslatomeSampleData)
    GOEnrichment(limma.DEGs,ontology="CC",classOfDEGs="up",
        test.method="classic", test.threshold = 0.05,mult.cor = TRUE)

[Package tRanslatome version 1.28.0 Index]