R/pathSim.R

In llrs/BioCor: Functional similarities

# pathSim ####
#' Calculates the Dice similarity between pathways
#'
#' Calculates the similarity between pathways using dice similarity score.
#' `diceSim` is used to calculate similarities between the two pathways.
#' @param pathway1,pathway2 A single pathway to calculate the similarity
#' @param info A GeneSetCollection or a list of genes and the pathways they are
#' involved.
#' @return The similarity between those pathways or all the similarities
#' between each comparison.
#' @seealso
#' [conversions()] help page to transform Dice score to Jaccard
#' score.
#' [mpathSim()] for multiple pairwise comparison of pathways.
#' @author Lluís Revilla
#' @export
#' @examples
#' if (require("reactome.db")) {
#'     # Extracts the paths of all genes of org.Hs.eg.db from reactome
#'     genes.react <- as.list(reactomeEXTID2PATHID)
#'     (paths <- sample(unique(unlist(genes.react)), 2))
#'     pathSim(paths[1], paths[2], genes.react)
#' } else {
#'     warning("You need reactome.db package for this example")
#' }
pathSim <- function(pathway1, pathway2, info) {
  if (length(pathway1) != 1 || length(pathway2) != 1) {
    stop(
      "Introduce just one pathway!\n",
      "If you want to calculate several similarities ",
      "between pathways use mpathSim"
    )
  }
  if (!is.character(pathway1) || !is.character(pathway2)) {
    stop("The input pathways should be characters")
  }
  if (!is.list(info)) {
    stop("info should be a list or a GeneSetCollection.\n
             See documentation.")
  }

  if (any(!c(pathway1, pathway2) %in% unlist(info, use.names = FALSE))) {
    return(NA)
  }

  # Invert the list
  rId <- unlist(info, use.names = FALSE)
  lId <- rep(names(info), lengths(info))
  pathways2genes <- split(lId, rId)

  # Convert the list
  pathways2genes <- list2env(pathways2genes)

  # Extract the gene ids for each pathway
  g1 <- pathways2genes[[pathway1]]
  g2 <- pathways2genes[[pathway2]]

  diceSim(g1, g2)
}

#' @describeIn pathSim Calculates all the similarities of a GeneSetCollection
#' and combine them using `combineScoresPar`
#' @export
setMethod(
  "pathSim",
  c(
    info = "GeneSetCollection", pathway1 = "character",
    pathway2 = "character"
  ),
  function(pathway1, pathway2, info) {
    if (length(pathway1) != 1 | length(pathway2) != 1) {
      stop(
        "Introduce just one pathway!\n",
        "If you want to calculate several similarities ",
        "between pathways use mpathSim"
      )
    }
    if (any(!c(pathway1, pathway2) %in% names(info))) {
      return(NA)
    }
    genes <- GSEABase::geneIds(info[c(pathway1, pathway2)])
    diceSim(genes[[1]], genes[[2]])
  }
)