load_genesets_syngo {goat}

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_20210225/syngo_ontologies.xlsx"
  if(file.exists(f)) genesets_asis = load_genesets_syngo(f)