R/bt_test_enrichment.R

In hancockinformatics/BacterialToolkit: Functions for working with bacterial projects

#' bt_test_enrichment
#'
#' @param query_genes Genes to be tested for enrichment.
#' @param enrichment_set Genes associated with a function/pathway.
#' @param total_genes Total number of genes.
#'
#' @return Raw p-value resulting from call to \code{stats::fisher.test()}.
#'
#' @export
#'
#' @description This function is designed to perform enrichment on a list of
#' genes of interest, comparing to some specified background. Uses Fisher's
#' Exact Test for p-value.
#'
#' @references None.
#'
#' @seealso https://github.com/hancockinformatics/BacterialToolkit
#'
#' @author Travis Blimkie
#'
bt_test_enrichment <- function(query_genes, enrichment_set, total_genes) {

  # Calculate overlap between the query list and enrichment set
  num_overlap <- as.numeric(length(dplyr::intersect(query_genes, enrichment_set)))


  # Construct the matrix to be used for the test
  enrichment_matrix <- matrix(c(
    num_overlap,
    as.numeric(length(enrichment_set) - num_overlap),
    as.numeric(length(query_genes) - num_overlap),
    as.numeric(total_genes - (length(enrichment_set) - num_overlap))
  ), nrow = 2, ncol = 2)


  # Run and return Fisher's Exact test on the matrix
  raw_pval <- stats::fisher.test(enrichment_matrix, alternative = "greater")$p.value

  return(raw_pval)

}