Add initial gene processing

process.R

@@ -0,0 +1,51 @@
+library(data.table)
+library(rlog)
+
+#' Process genes screening for a likely TPE-OLD.
+#'
+#' The return value will be a table containing genes and data to take in
+#' account when regarding them as TPE-OLD candidates.
+#'
+#' @param input Data from [`load_input()`].
+process_input <- function(input) {
+    results <- data.table(gene = input$genes$id)
+
+    # Exclude species with naturally or artificially short chromosomes as well
+    # as non-replicatively aging species.
+    species_ids <- input$species[
+        median_distance >= 7500000 & group == "replicative",
+        id
+    ]
+
+    gene_ids <- input$genes[, id]
+    gene_count <- length(gene_ids)
+
+    for (i in seq_along(gene_ids)) {
+        gene_id <- gene_ids[i]
+        log_info(sprintf("Processing gene %i/%i (%i)", i, gene_count, gene_id))
+
+        distances <- input$distances[
+            species %chin% species_ids & gene == gene_id,
+            .(species, distance)
+        ]
+
+        if (distances[, .N] < 12) {
+            next
+        }
+
+        clusters <- hclust(dist(distances[, distance]))
+        clusters_cut <- cutree(clusters, h = 1000000)
+        cluster <- distances[which(clusters_cut == 1)]
+
+        results[
+            gene == gene_id,
+            `:=`(
+                cluster_length = cluster[, .N],
+                cluster_mean = mean(cluster[, distance]),
+                cluster_species = list(cluster[, species])
+            )
+        ]
+    }
+
+    results
+}