R/fix_all_results.R

In ActiveDriverWGS: A Driver Discovery Tool for Cancer Whole Genomes

#' fix_all_results verifies that the results table has the correct format and p-values
#'
#' @param all_results a data frame containing the following columns
#' \describe{
#'     \item{id}{A string identifying the element of interest}
#'     \item{pp_element}{The p-value of the element}
#'     \item{element_muts_obs}{The number of patients with a mutation in the element}
#'     \item{element_muts_exp}{The expected number of patients with a mutation in the element with respect to background}
#'     \item{element_enriched}{A boolean indicating whether the element is enriched in mutations}
#'     \item{pp_site}{The p-value of the element}
#'     \item{site_muts_obs}{The number of patients with a mutation in the site}
#'     \item{site_muts_exp}{The expected number of patients with a mutation in the site with respect to element}
#'     \item{site_enriched}{A boolean indicating whether the site is enriched in mutations}
#'     \item{result_number}{A numeric indicator denoting the order in which the results were calculated}
#' }
#'
#' @return the same data frame
.fix_all_results = function(all_results) {

  resi = data.frame(all_results, stringsAsFactors=F)
  resi$pp_site = as.numeric(resi$pp_site)
  resi$pp_element = as.numeric(resi$pp_element)
  resi$element_muts_obs = as.numeric(resi$element_muts_obs)
  resi$element_muts_exp = as.numeric(resi$element_muts_exp)
  resi$element_enriched = as.logical(gsub("\\s+", "", resi$element_enriched))
  resi$site_muts_obs = as.numeric(resi$site_muts_obs)
  resi$site_muts_exp = as.numeric(resi$site_muts_exp)
  resi$site_enriched = as.logical(gsub("\\s+", "", resi$site_enriched))

  resi[!is.na(resi$pp_element) & resi$pp_element==0,"pp_element"] = 1e-300
  resi[!is.na(resi$pp_site) & resi$pp_site==0,"pp_site"] = 1e-300

  resi_tag = resi[,"id"]
  resi = resi[!duplicated(resi_tag),]
  resi
}

# @import stats

#' Returns significant results
#'
#' @param all_res a data frame containing the following columns
#' \describe{
#'     \item{id}{A string identifying the element of interest}
#'     \item{pp_element}{The p-value of the element}
#'     \item{element_muts_obs}{The number of patients with a mutation in the element}
#'     \item{element_muts_exp}{The expected number of patients with a mutation in the element with respect to background}
#'     \item{element_enriched}{A boolean indicating whether the element is enriched in mutations}
#'     \item{pp_site}{The p-value of the element}
#'     \item{site_muts_obs}{The number of patients with a mutation in the site}
#'     \item{site_muts_exp}{The expected number of patients with a mutation in the site with respect to element}
#'     \item{site_enriched}{A boolean indicating whether the site is enriched in mutations}
#'     \item{result_number}{A numeric indicator denoting the order in which the results were calculated}
#' }
#'
#' @return the same data frame with three addition columns
#' \describe{
#'     \item{fdr_element}{The FDR corrected p-value of the element}
#'     \item{fdr_site}{The FDR corrected p-value of the site}
#'     \item{has_site_mutations}{A V indicates the presence of site mutations}
#' }
#'
.get_signf_results = function(all_res) {
  this_results = all_res
  if (nrow(this_results)==0) {
    return(NULL)
  }
  # this is FDR treating element-level NAs as 1s
  this_results$fdr_element = stats::p.adjust(this_results$pp_element, method="fdr", n=nrow(this_results))

  this_results = this_results[order(this_results$fdr_element),]

  filtered_results = this_results[!is.na(this_results$fdr_element) & this_results$fdr_element<0.05,]
  unsignf_results = this_results[is.na(this_results$fdr_element) | this_results$fdr_element>=0.05,]

  if (nrow(filtered_results) + nrow(unsignf_results) != nrow(this_results)) {
    stop("Error: Something unexpected happened when formatting results")
  }

  if (nrow(filtered_results)!=0) {
    # site-level FDR perform only on elements with pre-selection of FDR<0.05
    filtered_results$fdr_site = stats::p.adjust(filtered_results$pp_site, method="fdr", n=nrow(filtered_results))
    filtered_results$has_site_mutations = !is.na(filtered_results$fdr_site) & filtered_results$fdr_site<0.05
    filtered_results$has_site_mutations = c("","V")[1+c(filtered_results$has_site_mutations)]
  }

  if (nrow(unsignf_results) !=0) {
    unsignf_results$fdr_site = NA
    unsignf_results$has_site_mutations = ""
  }

  final_results = rbind(filtered_results, unsignf_results)
  final_results$pp_element = replace(final_results$pp_element, which(is.na(final_results$pp_element)), 1)
  final_results$pp_site = replace(final_results$pp_site, which(is.na(final_results$pp_site)), 1)
  final_results$fdr_element = replace(final_results$fdr_element, which(is.na(final_results$fdr_element)), 1)
  final_results$fdr_site = replace(final_results$fdr_site, which(is.na(final_results$fdr_site)), 1)
  rownames(final_results) = NULL
  final_results
}