enrichment_analysis {BioNERO} | R Documentation

## Perform enrichment analysis for a set of genes

### Description

Perform enrichment analysis for a set of genes

### Usage

    enrichment_analysis(
      genes,
      background_genes,
      annotation,
      column = NULL,
      correction = "BH",
      p = 0.05,
      bp_param = BiocParallel::SerialParam()
    )

### Arguments

`genes` | Character vector containing genes for overrepresentation analysis.
`background_genes` | Character vector of genes to be used as background for the Fisher's Exact Test.
`annotation` | Annotation data frame with genes in the first column and functional annotation in the other columns. This data frame can be exported from Biomart or similar databases.
`column` | Column or columns of `annotation` to be used for enrichment. Both character or numeric values with column indices can be used. If users want to supply more than one column, input a character or numeric vector. Default: all columns from `annotation`.
`correction` | Multiple testing correction method. One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr" or "none". Default is "BH".
`p` | P-value threshold. P-values below this threshold will be considered significant. Default is 0.05.
`bp_param` | BiocParallel back-end to be used. Default: BiocParallel::SerialParam()

### Value

Data frame containing significant terms, p-values and associated genes.

### Author(s)

Fabricio Almeida-Silva

### Examples

    data(filt.se)
    data(zma.interpro)
    genes <- rownames(filt.se)[1:50]
    background_genes <- rownames(filt.se)
    annotation <- zma.interpro
    # Using p = 1 to show all results
    enrich <- enrichment_analysis(genes, background_genes, annotation, p = 1)

[Package BioNERO version 1.0.4 Index]