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 1.2.0 Index]