Reorganize source files and generalize presets

process/methods.R

@@ -0,0 +1,62 @@
+source("process/clusteriness.R")
+source("process/correlation.R")
+source("process/neural.R")
+source("process/proximity.R")
+
+#' Construct a new method.
+#'
+#' A method describes a way to perform a computation on gene distance data that
+#' results in a single score per gene. The function should accept the following
+#' parameters in this order:
+#'
+#'  - `distances` Distance data to use.
+#'  - `gene_ids` Genes to process.
+#'  - `preset` Preset to apply.
+#'
+#' The function should return a `data.table` with the following columns:
+#'
+#'  - `gene` Gene ID of the processed gene.
+#'  - `score` Score for the gene between 0.0 and 1.0.
+#'
+#' @param id Internal identifier for the method.
+#' @param name Human readable name for the method.
+#' @param description Short human readable description.
+#' @param fn Function to perform the computation.
+#'
+#' @return A named list containing the arguments.
+method <- function(id, name, description, fn) {
+    list(
+        id = id,
+        name = name,
+        description = description,
+        fn = fn
+    )
+}
+
+#' All methods to be included in the analysis.
+methods <- list(
+    method(
+        "clusteriness",
+        "Clustering",
+        "Clustering of genes",
+        process_clusteriness
+    ),
+    method(
+        "correlation",
+        "Correlation",
+        "Correlation with known genes",
+        process_correlation
+    ),
+    method(
+        "proximity",
+        "Proximity",
+        "Proximity to telomeres",
+        process_proximity
+    ),
+    method(
+        "neural",
+        "Neural",
+        "Assessment by neural network",
+        process_neural
+    )
+)