Add new correlation method

init.R

@@ -0,0 +1,97 @@
+source("clustering.R")
+source("correlation.R")
+source("input.R")
+source("util.R")
+
+# Load input data
+
+species <- run_cached("input/species", retrieve_species)
+genes <- run_cached("input/genes", retrieve_genes)
+
+distances <- run_cached(
+    "input/distances",
+    retrieve_distances,
+    species[, id],
+    genes[, id]
+)
+
+# Load processed data
+
+all_species <- species[, id]
+replicative_species <- species[replicative == TRUE, id]
+all_genes <- genes[, id]
+tpe_old_genes <- genes[suggested | verified == TRUE, id]
+
+clustering_all <- run_cached(
+    "all_species/clustering",
+    process_clustering,
+    distances,
+    all_species,
+    all_genes
+)
+
+clustering_replicative <- run_cached(
+    "replicative_species/clustering",
+    process_clustering,
+    distances,
+    replicative_species,
+    all_genes
+)
+
+correlation_all <- run_cached(
+    "all_species/correlation",
+    process_correlation,
+    distances,
+    all_species,
+    all_genes,
+    tpe_old_genes
+)
+
+correlation_replicative <- run_cached(
+    "replicative_species/correlation",
+    process_correlation,
+    distances,
+    replicative_species,
+    all_genes,
+    tpe_old_genes
+)
+
+# Merge processed data as well as gene information.
+
+results_all <- merge(
+    genes,
+    clustering_all,
+    by.x = "id",
+    by.y = "gene"
+)
+
+results_all <- merge(
+    results_all,
+    correlation_all,
+    by.x = "id",
+    by.y = "gene"
+)
+
+results_replicative <- merge(
+    genes,
+    clustering_replicative,
+    by.x = "id",
+    by.y = "gene"
+)
+
+results_replicative <- merge(
+    results_replicative,
+    correlation_replicative,
+    by.x = "id",
+    by.y = "gene"
+)
+
+# Rename `id` columns to `gene`.
+
+setnames(results_all, "id", "gene")
+setnames(results_replicative, "id", "gene")
+
+# Order results by cluster length descendingly as a start.
+
+setorder(results_all, -cluster_length)
+setorder(results_replicative, -cluster_length)