load_genesets_syngo: parse genesets from the SynGO database

In goat: Gene Set Analysis Using the Gene Set Ordinal Association Test

parse genesets from the SynGO database

Description

Workflow;

• obtain the input file from; https://www.syngoportal.org

• click "bulk download SynGO release ..." for SynGO release of interest

• unzip

• call this function with the full file path to the 'syngo_ontologies.xlsx' file

Usage

load_genesets_syngo(filename, gene_database = "entrez")

Arguments

filename	full path to the "syngo_ontologies.xlsx" file that was extracted from a SynGO bulk download ZIP archive
gene_database	gene IDs to return. must be any of; "entrez" (default), "hgnc", "ensembl"

Value

table with columns; source (character), source_version (character), id (character), name (character), genes (list), ngenes (int)

Examples

  # TODO: update the filename to your downloaded file
  f = "C:/DATA/SynGO_bulk_download_release_20231201/syngo_ontologies.xlsx"
  if(file.exists(f)) genesets_asis = load_genesets_syngo(f)

goat documentation built on April 3, 2025, 6:05 p.m.