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The FunctionalEnrichment class

Source: R/AllClasses.R, R/show-methods.R
FunctionalEnrichment-class.Rd

This class introduces the possibility to store the results of functional enrichment analyses such as over-representation analysis (ORA), gene set enrichment analysis (GSEA), and competitive gene set test accounting for inter-gene correlation (CAMERA). The different slots contained in this class are used to store enrichment results generated through the enrichGenes() function.

Usage

# S4 method for class 'FunctionalEnrichment'
enrichmentResults(object)

# S4 method for class 'FunctionalEnrichment'
enrichmentDatabase(object)

# S4 method for class 'FunctionalEnrichment'
enrichmentMethod(object)

# S4 method for class 'FunctionalEnrichment'
geneSet(object)

# S4 method for class 'FunctionalEnrichment'
enrichmentMetric(object)

# S4 method for class 'FunctionalEnrichment'
enrichedFeatures(object)

# S4 method for class 'FunctionalEnrichment'
show(object)

Arguments

object

An object of class FunctionalEnrichment containing enrichment results

Value

  • the enrichmentResults() function returns a data.frame object with the results of the functional enrichment analysis.

  • the enrichmentDatabase() function returns a character that specifies the database that provided the gene-set collection.

  • the enrichmentMethod() function returns a character with the enrichment method used for the analysis.

  • the geneSet() function returns a list with the gene-set collections retrieved.

  • the enrichmentMetric() function returns a numeric object with ranked gene statistic used for GSEA.

  • the enrichmentMetric() function returns a character object with the names of the ranked features used for GSEA.

Functions

  • enrichmentResults(FunctionalEnrichment): Access the data slot to take a closer look at all the enriched terms of an enrichment analysis

  • enrichmentDatabase(FunctionalEnrichment): See the database used for the functional enrichment

  • enrichmentMethod(FunctionalEnrichment): Visualize the approach used for the functional enrichment analysis

  • geneSet(FunctionalEnrichment): Access the geneSet slot to see the collection of gene sets used for GSEA

  • enrichmentMetric(FunctionalEnrichment): View the ranking metric used for GSEA

  • enrichedFeatures(FunctionalEnrichment): View the names of the pre-ranked features used for GSEA

  • show(FunctionalEnrichment): Show method for objects of class FunctionalEnrichment

Slots

data

A data.frame object holding the output of enrichment analysis

method

The method used to perform functional enrichment analysis (e.g. Gene Set Enrichment Analysis (GSEA))

organism

The name of the organism under consideration (e.g. Homo sapiens)

database

The name of the database used for the enrichment analysis (e.g. KEGG)

pCutoff

A numeric value defining the threshold used for statistical significance in the enrichment analysis (e.g. 0.05)

pAdjustment

A character indicating the method used to correct p-values for multiple testing (e.g. fdr)

features

A character vector containing the list of features used for the enrichment

statistic

A numeric vector containing the statistic used to run GSEA. This parameter is empty for ORA and CAMERA

universe

The background universe of features. Typically, this is equal to the complete list of features assayed. This slot is NULL for GSEA

geneSet

The gene set used for the functional enrichment analysis. It is a list object where each element contains the list of genes belonging to a specific pathway.

Author

Jacopo Ronchi, jacopo.ronchi@unimib.it