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R/proximity.R

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+# 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.
+proximity <- function(distances, preset) {
+    # Prefilter distances by species and gene.
+    distances <- distances[
+        species %chin% preset$species_ids & gene %chin% preset$gene_ids
+    ]
+
+    # Compute the score as described above.
+
+    distances <- distances[, .(mean_distance = mean(distance)), by = "gene"]
+    max_distance <- distances[, max(mean_distance)]
+    distances[, score := 1 - mean_distance / max_distance]
+
+    distances[, .(gene, score)]
+}