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

BP, CC, MF (i.e. Gene Ontology) and REACTOME enrichment analyses for a list of genes of interest, given a list of background genes.

The package supports ENTREZIDs (default), GENE SYMBOLs and UNIPROT accessions.

Installation

1. Install the devtools package from CRAN if you haven't done so:

install.packages("devtools")

1. Load the devtools package:

library("devtools")

1. Install FunEnrich using the install_github function:

install_github("galanisl/FunEnrich")

Usage

To start using FunEnrich, load the package:

library("FunEnrich")

Let's now use the gene-disease associations included in the package. We will use disease.genes as background and genes associated with metabolic disorders as genes of interest (type ?metabolic and ?disease.genes in R for more information about these datasets):

analysis <- fun_enrich(gene.list = metabolic, background = disease.genes, 
                       id.type = "ENTREZID", benjamini = FALSE)

We can now explore, for example, the Molecular Functions enriched in genes that are specifically associated with metabolic disorders...

head(analysis$mf)

... as well as the enriched REACTOME pathways:

head(analysis$reactome)

It is also possible to generate a bar plot that focuses on the most enriched term of one or all categories:

plot_fun_enrich(enr = analysis, aspect = "ALL", benjamini = F, 
                top = 5, char_per_line = 80)

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