preset: Turn into S3 class

R/preset.R

@@ -0,0 +1,66 @@
+#' Create a new preset.
+#'
+#' A preset is used to specify which methods and inputs should be used for an
+#' analysis. Note that the genes to process should normally include the
+#' reference genes to be able to assess the results later.
+#'
+#' Available methods are:
+#'
+#'  - `clusteriness` How much the gene distances cluster across species.
+#'  - `correlation` The mean correlation with the reference genes.
+#'  - `proximity` Mean proximity to telomeres.
+#'  - `neural` Assessment by neural network.
+#'
+#' @param methods Methods to apply.
+#' @param species_ids IDs of species to include.
+#' @param gene_ids IDs of genes to screen.
+#' @param reference_gene_ids IDs of reference genes to compare to.
+#'
+#' @return The preset to use with [analyze()].
+#'
+#' @export
+preset <- function(methods = c(
+                       "clusteriness",
+                       "correlation",
+                       "neural",
+                       "proximity"
+                   ),
+                   species_ids = NULL,
+                   gene_ids = NULL,
+                   reference_gene_ids = NULL) {
+    # The included data gets sorted to be able to produce predictable hashes
+    # for the object later.
+    structure(
+        list(
+            methods = sort(methods),
+            species_ids = sort(species_ids),
+            gene_ids = sort(gene_ids),
+            reference_gene_ids = sort(reference_gene_ids)
+        ),
+        class = "geposan_preset"
+    )
+}
+
+#' S3 method to print a preset object.
+#'
+#' @seealso [preset()]
+#'
+#' @export
+print.geposan_preset <- function(preset, ...) {
+    cat("geposan preset:")
+    cat("\n  Included methods: ")
+    cat(preset$method_ids, sep = ", ")
+
+    cat(sprintf(
+        "\n  Input data: %i species, %i genes",
+        length(preset$species_ids),
+        length(preset$gene_ids)
+    ))
+
+    cat(sprintf(
+        "\n  Comparison data: %i reference genes\n",
+        length(preset$reference_gene_ids)
+    ))
+
+    invisible(preset)
+}