RunEnrichr: Perform enrichment analyses for a gene list

In j-andrews7/EZscRNA: Simple Convenience Functions for High-Level scRNA-Seq Analysis

Description

RunEnrichr submits gene lists to the enrichr web server for gene ontology/pathway enrichment analyses and collects the results as a named list for each library used.

Usage

RunEnrichr(genes, libraries = c("GO_Molecular_Function_2018",
  "GO_Cellular_Component_2018", "GO_Biological_Process_2018",
  "KEGG_2019_Human", "Reactome_2016", "BioCarta_2016", "Panther_2016"),
  outdir = NULL)

Arguments

genes	A vector of gene symbols that will be tested.
libraries	A vector of libraries to test the genes against.
outdir	Path to output directory. If specified, tables for each library will be saved.

Details

Potential libraries can be viewed with listEnrichrDbs from the enrichR package.

The enrichr web server can be found at https://amp.pharm.mssm.edu/Enrichr/. If you use this function, you should be sure to cite the original authors.

Value

A named list of enrichment results for each library.

References

Kuleshov MV, Jones MR, Rouillard AD, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016; gkw377

See Also

VizEnrichments for visualization.

Examples

genes <- c("CD8A", "CD4", "FOXP3", "CTLA4", "GNLY", "TNFSF18", "TNFRSF18", 
  "CXCR4", "CD3E", "CCR6", "CCR7", "IL7R")
libs <- c("Reactome_2016", "KEGG_2019_HUMAN")
enrichments <- RunEnrichr(genes, libraries = libs)

j-andrews7/EZscRNA documentation built on Feb. 24, 2020, 10:37 a.m.