EnrichedSets-class {tRanslatome} | R Documentation

## Class `EnrichedSets`

### Description

A class generated from the function `RegulatoryEnrichment()` containing the overrepresented post-transcriptional regulatory factors (RBPs, miRNAs, etc) 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 regulatory enrichment analysis. The data frame contains one row for each regulatory factor, while columns are organized as follows:

  1. `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`.

  2. `ID`, ID of the regulatory factor.

  3. `number`, number of genes in the human genome associated to the regulatory factor.

  4. `list`, list of genes in the list of DEGs associated to the regulatory factor.

  5. `pv.fisher`, enrichment p-value calculated with the Fisher test.

  6. `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 = "EnrichedSets")`: displays the slot `enriched.table`.

label.level.enriched

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

### Methods

Heatmap

  `signature(object = "EnrichedSets")`: enables the generation of a heatmap of the top enriched regulatory factors for the first and second level of analysis.

label.level.enriched

  `signature(object = "EnrichedSets")`: displays the slot `label.level.enriched`.

Radar

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

show

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

### Author(s)

Erik Dassi, Toma Tebaldi

### References

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. Dassi E et al(2012). AURA: Atlas of UTR Regulatory Activity. Bioinformatics. 28(1):142-4.

### See Also

`GOsets` `DEGs`

### Examples

    showClass("EnrichedSets")

[Package tRanslatome version 1.25.1 Index]