R/simGO.R

In GangLiLab/genekitr: Gene Analysis Toolkit

#' Simplify GO enrichment result
#'
#' The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product
#' attributes across all species.
#'
#' @param enrich_df GO enrichment analysis of `genORA()` result.
#' @param sim_method Method of calculating the similarity between nodes, one of one of "Resnik",
#' "Lin", "Rel", "Jiang" , "Wang" methods.
#' @param org  Organism name from `biocOrg_name`.
#' @param ont  One of "bp", "mf", and "cc".
#'
#' @importFrom dplyr arrange distinct pull
#'
#' @return A `data.frame` contains simplified GO terms.
#' @export
#'
simGO <- function(enrich_df,
                  sim_method = c("Resnik", "Lin", "Rel", "Jiang", "Wang"),
                  org = NULL,
                  ont = NULL) {
  sim_method <- match.arg(sim_method)

  simterm <- get_sim_data(enrich_df,
    sim_method = sim_method,
    org = org, ont = ont
  ) %>%
    .[["r"]] %>%
    dplyr::arrange(cluster) %>%
    dplyr::distinct(parent, .keep_all = TRUE) %>%
    dplyr::pull(go)

  egosim <- enrich_df %>% dplyr::filter(.[[1]] %in% simterm)


  return(egosim)
}