R/do_enrichr_pod.R

In CogDisResLab/BioPathNet: BioPathNet: Three Pod Analysis System

#' Perform the EnrichR Analysis
#'
#' This function takes in a BPNList object and returns a BPNList object with the
#' enrichr slot updated with process EnrichR Results
#'
#' This function takes in a BPNList object and returns a BPNList object with the
#' enrichr slot updated with process EnrichR Results.
#'
#' @param bpn BPNList An object of class BPNList created from \link{prepare_data}
#' @param alpha numeric The Alpha value for statistical significance. Defaults to 0.05.
#' @param lower numeric The cutoff for down-regulated genes. If not specified, it takes the bottom 10\% of the
#' @param upper numeric The cutoff for up-regulated genes. If not specified, it takes the top 10\% of the dataset
#' @param useFDR logical Whether to filter by adjusted p-value
#'
#' @return An object of class BPNList with its enrichr slot populated with the results
#' @export
#'
#' @import purrr enrichR
#' @importFrom rlang .data
#' @importFrom stats quantile
#' @import dplyr
#'
#' @examples
#' TRUE
do_enrichr_pod <- function(bpn, alpha = 0.05, lower = NULL, upper = NULL, useFDR=TRUE) {

  inp <- input(bpn)

  if (is.null(lower)) {
    lower <- round(stats::quantile(inp$Value_LogDiffExp, 0.10), 3)
  }

  if (is.null(upper)) {
    upper <- round(stats::quantile(inp$Value_LogDiffExp, 0.90), 3)
  }

  dbs <- c("GO_Biological_Process_2023",
           "GO_Molecular_Function_2023",
           "GO_Cellular_Component_2023")

  columns <- c("Biological_Process",
               "Molecular_Function",
               "Cellular_Component")

  upreg <- inp %>%
    filter(.data$Value_LogDiffExp >= upper) %>%
    dplyr::filter(.data$Significane_pvalue <= alpha)

  downreg <- inp %>%
    filter(.data$Value_LogDiffExp <= lower) %>%
    dplyr::filter(.data$Significane_pvalue <= alpha)

  #TODO Make a test for enrichR being live here
  options(enrichR.base.address = "http://amp.pharm.mssm.edu/Enrichr/")
  options(enrichR.live = TRUE)

  up_enrichr <- upreg %>%
    pull(.data$Name_GeneSymbol) %>%
    enrichR::enrichr(databases = dbs) %>%
    map2(columns, ~ mutate(.x, namespace = .y)) %>%
    bind_rows

  down_enrichr <- downreg %>%
    pull(.data$Name_GeneSymbol) %>%
    enrichR::enrichr(databases = dbs) %>%
    map2(columns, ~ mutate(.x, namespace = .y)) %>%
    bind_rows

  e <- EnrichRResult(
    up_enrichr, down_enrichr, upreg, downreg, alpha, upper, lower, dbs, useFDR
  )

  enrichr(bpn) <- e

  bpn
}