Add cross-validation function

NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(print,geposan_comparison)
 S3method(print,geposan_preset)
+S3method(print,geposan_validation)
 export(analyze)
 export(compare)
 export(optimal_weights)

R/validate.R

@@ -0,0 +1,108 @@
+#' Perform cross-validation for the analysis.
+#'
+#' This function reoptimizes the analysis leaving out one of the original
+#' reference genes at a time.
+#'
+#' @param analysis The analysis to validate.
+#' @param progress An optional progress function that should accept a single
+#'   value between 0.0 and 1.0 for progress information.
+#'
+#' @returns An object containing the mean absolute error and the mean percent
+#'   rank for the original analysis as well as the validation.
+#'
+#' @export
+validate <- function(analysis, progress = NULL) {
+    if (class(analysis) != "geposan_analysis") {
+        stop("Analysis is invalid. Use geposan::analyze().")
+    }
+
+    cached("validation", analysis$preset, {
+        reference_gene_ids <- analysis$preset$reference_gene_ids
+        n_references <- length(reference_gene_ids)
+        methods <- analysis$preset$methods
+        ranking_reference <- analysis$ranking
+        n_ranks <- nrow(ranking_reference)
+
+        mean_error_reference <- mean(
+            1.0 - ranking_reference[gene %chin% reference_gene_ids, score]
+        )
+
+        mean_rank_reference <- mean(
+            1.0 - ranking_reference[gene %chin% reference_gene_ids, rank] /
+                n_ranks
+        )
+
+        mean_error_validation <- 0.0
+        mean_rank_validation <- 0.0
+
+        progress_state <- 0.0
+        progress_step <- 1.0 / n_references
+
+        for (validation_gene_id in reference_gene_ids) {
+            included_gene_ids <- reference_gene_ids[
+                reference_gene_ids != validation_gene_id
+            ]
+
+            weights <- optimal_weights(
+                analysis,
+                methods,
+                included_gene_ids
+            )
+
+            ranking_validation <- ranking(analysis, weights)
+
+            mean_error_validation <- mean_error_validation +
+                (1.0 - ranking_validation[gene == validation_gene_id, score]) /
+                    n_references
+
+            mean_rank_validation <- mean_rank_validation +
+                (1.0 - ranking_validation[gene == validation_gene_id, rank] /
+                    n_ranks) / n_references
+
+            if (!is.null(progress)) {
+                progress_state <- progress_state + progress_step
+                progress(progress_state)
+            }
+        }
+
+        structure(
+            list(
+                mean_error_reference = mean_error_reference,
+                mean_error_validation = mean_error_validation,
+                mean_rank_reference = mean_rank_reference,
+                mean_rank_validation = mean_rank_validation
+            ),
+            class = "geposan_validation"
+        )
+    })
+}
+
+#' S3 method to print a validation object.
+#'
+#' @param x The validation to print.
+#' @param ... Other parameters.
+#'
+#' @seealso [validate()]
+#'
+#' @export
+print.geposan_validation <- function(x, ...) {
+    cat("geposan validation:\n")
+    cat(sprintf(
+        paste0(
+            "\n  Absolute scores:",
+            "\n  Mean error reference:  %.3f",
+            "\n  Mean error validation: %.3f",
+            "\n",
+            "\n  Ranks:",
+            "\n  Mean rank reference:   %.1f%%",
+            "\n  Mean rank validation:  %.1f%%",
+            "\n"
+        ),
+        x$mean_error_reference,
+        x$mean_error_validation,
+        x$mean_rank_reference * 100,
+        x$mean_rank_validation * 100
+    ))
+
+    invisible(x)
+}

man/print.geposan_validation.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/validate.R
+\name{print.geposan_validation}
+\alias{print.geposan_validation}
+\title{S3 method to print a validation object.}
+\usage{
+\method{print}{geposan_validation}(x, ...)
+}
+\arguments{
+\item{x}{The validation to print.}
+
+\item{...}{Other parameters.}
+}
+\description{
+S3 method to print a validation object.
+}
+\seealso{
+\code{\link[=validate]{validate()}}
+}

man/validate.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/validate.R
+\name{validate}
+\alias{validate}
+\title{Perform cross-validation for the analysis.}
+\usage{
+validate(analysis, progress = NULL)
+}
+\arguments{
+\item{analysis}{The analysis to validate.}
+
+\item{progress}{An optional progress function that should accept a single
+value between 0.0 and 1.0 for progress information.}
+}
+\value{
+An object containing the mean absolute error and the mean percent
+rank for the original analysis as well as the validation.
+}
+\description{
+This function reoptimizes the analysis leaving out one of the original
+reference genes at a time.
+}