Reorganize source files and generalize presets

methods.R

@@ -1,63 +0,0 @@
-source("clusteriness.R")
-source("correlation.R")
-source("neural.R")
-source("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.
-#'  - `species_ids` Species, whose data should be included.
-#'  - `gene_ids` Genes to process.
-#'  - `reference_gene_ids` Genes to compare to.
-#'
-#' 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
-    )
-)