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Read a Custom Ontology File

read_ontology.Rd

Reads a user-supplied ontology into the TERM2GENE and optional TERM2NAME structures required by clusterProfiler::enricher() and clusterProfiler::GSEA().

Supported formats are:

  • GMT files, where each line is term, name, then one or more gene IDs

  • Delimited text files (csv or tsv) with either:

    • 2 columns: term, gene

    • 3 columns: term, name, gene

Gene identifiers in uploaded ontologies must match the identifiers used for enrichment. In the ProtPipe Shiny app, this currently means Entrez gene IDs.

Usage

read_ontology(file)

Arguments

file

Path to a .gmt, .csv, or .tsv ontology file.

Value

A named list with term2gene and term2name.