fun_enrich: Perform BP, CC, MF and REACTOME enrichment analyses

In galanisl/FunEnrich: GO and Pathway enrichment analyses for genes of interest

Description

Given a list of genes of interest and a reference background, performs a Fisher's test for the over-representation of Gene Ontology terms and REACTOME pathways in the former.

Usage

fun_enrich(gene.list, background, id.type = "ENTREZID", benjamini = F)

Arguments

gene.list	character; A vector with the genes of interest.
background	character; A vector with the background list of genes.
id.type	character; One of ENTREZID (default), SYMBOL or UNIPROT accession. This is the ID type of gene.list and background.
benjamini	logical; Whether to include Benjamini-Hochberg adjusted p-values or not.

Value

A list with four data frames, one per enrichment analysis:

bp	Contains the Biological Process go.ids annotating the genes of interest, together with their term description, p-values pval and Benjamini-Hochberg adjusted p-values bh if requested. In the latter case, the data frame is sorted by corrected p-value.
cc	Same as bp but for Cellular Compartment.
mf	Same as bp but for Molecular Function.
reactome	Same as the rest but the first column is react.id instead of go.id.

Author(s)

Gregorio Alanis-Lobato [e-mail]

Examples

# Use the included lists of disease genes and genes associated with metabolic
# disorders as background and genes of interest, respectively
analysis <- fun_enrich(gene.list = metabolic, background = disease.genes, 
                      id.type = "ENTREZID", benjamini = TRUE)

galanisl/FunEnrich documentation built on May 5, 2019, 3:49 a.m.