R/get_ids.R

In GOfuncR: Gene ontology enrichment using FUNC

## return the IDs and names of GO-categories that match ONE name

get_ids = function(go_name, term_df=NULL, godir=NULL){
    
    # check if term is user-defined or get the integrated version
    term = eval_term(term_df, godir)
    
    if(length(go_name)!=1){
        stop("Please use a single GO-category name.")
    }
    # remove obsolete
    term = term[term[,5]==0,]
    # grep for name
    out = term[grep(go_name, term[,2], ignore.case=TRUE),2:4]
    if(nrow(out)==0){
        stop("No matches found.")
    }
    out = out[order(out[,2], out[,3]),]
    rownames(out) = 1:nrow(out)
    colnames(out) = c("node_name", "root_node", "go_id")
    
    return(out)
}