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

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

Arguments

organism_db

character(1): 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

character(1): 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

character(1) | NULL: 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.

Examples

# Minimal real example (runs only if org package is installed)
tmp <- tempdir()
if (requireNamespace("org.Mm.eg.db", quietly = TRUE) &&
    requireNamespace("AnnotationDbi", quietly = TRUE)) {
    gs <- extract_gene_sets(
        organism_db = "org.Mm.eg.db",
        output_dir  = tmp,
        filename    = "mm_genesets.tsv"
    )
    head(gs)
    # The file path:
    file.path(tmp, "mm_genesets.tsv")
}
#> 
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 
#> Download complete! The file has been saved as: /tmp/RtmpD8INMF/mm_genesets.tsv
#> [1] "/tmp/RtmpD8INMF/mm_genesets.tsv"

# If the organism package is not installed, you can still see the TSV format:
tiny <- data.frame(
    DB = c("GO_BP", "GO_MF"),
    Geneset = c("GO:0008150", "GO:0003674"),
    Gene = c("Trp53", "Egfr"),
    stringsAsFactors = FALSE
)
utils::write.table(
    tiny,
    file = file.path(tmp, "example_genesets.tsv"),
    sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE
)