enrichment_analysis: Perform overrepresentation analysis for a set of genes

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

Perform overrepresentation analysis for a set of genes

Description

Perform overrepresentation analysis for a set of genes

Usage

enrichment_analysis(
  genes,
  background_genes,
  annotation,
  column = NULL,
  correction = "BH",
  p = 0.05,
  min_setsize = 10,
  max_setsize = 500,
  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 overrepresentation analysis.
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: 0.05.
min_setsize	Numeric indicating the minimum gene set size to be considered. Gene sets correspond to levels of each variable in annotation). Default: 10.
max_setsize	Numeric indicating the maximum gene set size to be considered. Gene sets correspond to levels of each variable in annotation). Default: 500.
bp_param	BiocParallel back-end to be used. Default: BiocParallel::SerialParam()

Value

A data frame of overrepresentation results with the following variables:

term

character, functional term ID/name.

genes

numeric, intersection length between input genes and genes in a particular functional term.

all

numeric, number of all genes in a particular functional term.

pval

numeric, P-value for the hypergeometric test.

padj

numeric, P-value adjusted for multiple comparisons using the method specified in parameter adj.

category

character, name of the grouping variable (i.e., column name of annotation).

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)

almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.