Download Enrichr databases — download_enrichr

Download gene sets from one or more Enrichr libraries and return them as a table with one row per gene-set membership.

If output_dir is provided, the same table is also written to disk as a tab-separated file (.tsv). If filename is NULL, a timestamped name is generated to ensure uniqueness.

Usage

download_enrichr_databases(gene_set_lib, output_dir = NULL, filename = NULL)

Arguments

gene_set_lib: character(). A character vector of Enrichr library names to download, e.g. c("WikiPathways_2019_Human", "NCI-Nature_2016").
output_dir: character(1) or NULL. Output directory for writing a .tsv file. If NULL, no file is written.
filename: character(1) or NULL. Output file name (not a path). If NULL and output_dir is not NULL, a default name of the form enrichr_databases_YYYYmmdd-HHMMSS.tsv is used. Due to commas in some terms, .tsv is recommended.

Value

A data.frame with three columns:

DB: Enrichr library name.
Geneset: Gene set or pathway term within that library.
Gene: Gene symbol contained in the gene set.

If a requested library cannot be downloaded, it may be omitted from the result. The function errors if no gene sets can be retrieved.

Examples

if (interactive()) {
  libs <- c("WikiPathways_2019_Human")
  out <- download_enrichr_databases(
    gene_set_lib = libs,
    output_dir = tempdir(),
    filename = "enrichr_demo.tsv"
  )
  head(out)
}