From ac9894e988cfe3bd471a1bfedd9e634a172fa253 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Sun, 9 Jan 2022 19:52:47 +0100
Subject: [PATCH] proximity: Remove method

---
 NAMESPACE        |  1 -
 R/method.R       |  3 +--
 R/proximity.R    | 39 ---------------------------------------
 man/proximity.Rd | 15 ---------------
 4 files changed, 1 insertion(+), 57 deletions(-)
 delete mode 100644 R/proximity.R
 delete mode 100644 man/proximity.Rd

diff --git a/NAMESPACE b/NAMESPACE
index cc7f389..49d5bdf 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -21,7 +21,6 @@ export(plot_positions)
 export(plot_rankings)
 export(plot_scores)
 export(preset)
-export(proximity)
 export(ranking)
 export(result)
 export(validate)
diff --git a/R/method.R b/R/method.R
index a1257f4..c0be5ad 100644
--- a/R/method.R
+++ b/R/method.R
@@ -36,8 +36,7 @@ all_methods <- function() {
         clustering(),
         correlation(),
         neural(),
-        adjacency(),
-        proximity()
+        adjacency()
     )
 }
 
diff --git a/R/proximity.R b/R/proximity.R
deleted file mode 100644
index 70c6d92..0000000
--- a/R/proximity.R
+++ /dev/null
@@ -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)]
-                )
-            })
-        }
-    )
-}
diff --git a/man/proximity.Rd b/man/proximity.Rd
deleted file mode 100644
index fa8d822..0000000
--- a/man/proximity.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/proximity.R
-\name{proximity}
-\alias{proximity}
-\title{Score the mean distance of genes to the telomeres across species.}
-\usage{
-proximity()
-}
-\value{
-An object of class \code{geposan_method}.
-}
-\description{
-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.
-}