Download Gene Set Annotations from Bioconductor Organism Databases

This function extracts gene-to-ontology mappings from a specified Bioconductor organism annotation package (e.g., `org.Hs.eg.db`, `org.Mm.eg.db`) and saves the gene sets to a `.tsv` file in a standardized format. The output includes mappings for Gene Ontology (GO) Biological Process (BP), Molecular Function (MF), Cellular Component (CC), and KEGG pathways. The resulting file can be used directly with enrichment functions such as `clusterProfiler::enricher()` with `TERM2GENE`.

Usage

download_bioconductor_database(
  organism_db = "org.Hs.eg.db",
  output_dir = here::here(),
  filename = NULL
)

Arguments

organism_db

A string specifying the Bioconductor organism annotation database to use (e.g., `"org.Hs.eg.db"` for human or `"org.Mm.eg.db"` for mouse).

output_dir

A string specifying the output directory where the `.tsv` file will be saved. Defaults to the current project directory as defined by `here::here()`.

filename

An optional string specifying the filename for the output file. If `NULL` (default), a filename is generated automatically with a timestamp.

Value

A `data.frame` of gene set annotations with three columns:

DB

Ontology/database source, e.g. `"GO_BP"`, `"GO_MF"`, `"GO_CC"`, or `"KEGG"` (if available).

Geneset

Ontology term ID or pathway ID (e.g. GO ID, KEGG ID).

Gene

Gene symbol (SYMBOL).

Details

The TSV has three columns:

DB

Ontology/database source, e.g., "GO_BP", "GO_MF", "GO_CC", or "KEGG" (if available).

Geneset

Ontology term ID or pathway ID (e.g., GO ID, KEGG ID).

Gene

Gene symbol (SYMBOL).

Note: Some org.*.eg.db packages no longer include KEGG mappings; in such cases the KEGG section will be empty.

In addition to returning the `data.frame`, the function also writes the same table to disk as a `.tsv` file in the specified `output_dir`.