GOsets-class {tRanslatome} | R Documentation

## Class `GOsets`

### Description

A class generated from the function `GOEnrichment()` containing the overrepresented Gene Ontology terms from the lists of differentially expressed genes coming from the analysis of two different expression levels.

### Slots

`enriched.table`:

  Object of class `data.frame` containing all the GO enrichment analysis. The data frame contains one row for each GO term, while columns are organized as follows:

  1. `ontology`, GO ontology of the term, either `BP`,`CC` or `MF`.

  2. `level`, level of analysis on which the enrichment is calculated. The names of the two levels are taken from the object `DEGs` given as an input to the function `GOEnrichment`.

  3. `GO.ID`, Gene Ontology accession ID of the term.

  4. `term`, Gene Ontology name of the term.

  5. `annotated`, number of genes in the human genome associated to the GO term.

  6. `significant`, number of genes in the list of DEGs associated to the GO term.

  7. `expected`, number of genes in the list of DEGs expected to be associated to the GO term by chance.

  8. `expected`, number of genes in the list of DEGs expected to be associated to the GO term by chance.

  9. `pv.fisher`, enrichment p-value calculated with the Fisher test. The result is dependent on the method chosen to calculate enrichment(`classic`,`elim`, `weight`,`weight01` or `parentchild`).

  10. `pv.fisher.BH`, the Benjamini-Hochberg corrected enrichment p-value calculated with the Fisher test according to the chosen enrichment method.

`label.level.enriched`:

  Object of class `character` specifying the names of the two levels compared in the experiment.

### Accessors

enriched.table

  `signature(object = "GOsets")`: displays the slot `enriched.table`.

label.level.enriched

  `signature(object = "GOsets")`: displays the slot `label.level.enriched`, slot of class `character` specifying the names of the two levels compared in the experiment.

### Methods

GOComparison

  `signature(object = "GOsets")`: returns an object of class `GOsims`, containing identity and semantic similarity comparisons among the enriched GO terms.

Heatmap

  `signature(object = "GOsets")`: enables the generation of a heatmap of the top enriched GO terms for the first and second level of analysis.

Radar

  `signature(object = "GOsets")`: enables the generation of a radar plot of the top enriched GO terms for the first and second level of analysis.

show

  `signature(object = "GOsets")`: displays all the two slots of the class.

### 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

`EnrichedSets` `GOComparison` `DEGs`

### Examples

    showClass("GOsets")

[Package tRanslatome version 1.28.0 Index]