proximity: Use median distance by default

R/proximity.R

@@ -1,39 +0,0 @@
-#' Score the mean distance of genes to the telomeres across species.
-#'
-#' A score will be given to each gene such that 0.0 corresponds to the maximal
-#' mean distance across all genes and 1.0 corresponds to a distance of 0.
-#'
-#' @return An object of class `geposan_method`.
-#'
-#' @export
-proximity <- function() {
-    method(
-        id = "proximity",
-        name = "Proximity",
-        description = "Proximity to telomeres",
-        function(preset, progress) {
-            species_ids <- preset$species_ids
-            gene_ids <- preset$gene_ids
-
-            cached("proximity", c(species_ids, gene_ids), {
-                # Prefilter distances by species and gene.
-                data <- geposan::distances[
-                    species %chin% preset$species_ids &
-                        gene %chin% preset$gene_ids
-                ]
-
-                # Compute the score as described above.
-                data <- data[, .(mean_distance = mean(distance)), by = "gene"]
-                max_distance <- data[, max(mean_distance)]
-                data[, score := 1 - mean_distance / max_distance]
-
-                progress(1.0)
-
-                result(
-                    method = "proximity",
-                    scores = data[, .(gene, score)]
-                )
-            })
-        }
-    )
-}