From 7d3bedb4368a63838ae6a825afeffc5168df7c09 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Sun, 21 Nov 2021 23:56:15 +0100
Subject: [PATCH] ranking: Add optimization for median

---
 R/preset.R  | 1 +
 R/ranking.R | 8 +++++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/R/preset.R b/R/preset.R
index 441082c..cc21615 100644
--- a/R/preset.R
+++ b/R/preset.R
@@ -24,6 +24,7 @@
 #' Available optimization targets are:
 #'
 #'  - `mean` Mean rank of the reference genes.
+#'  - `median` Median rank of the reference genes.
 #'  - `max` First rank of the reference genes.
 #'  - `min` Last rank of the reference genes.
 #'
diff --git a/R/ranking.R b/R/ranking.R
index 67d52d4..0dcbfa7 100644
--- a/R/ranking.R
+++ b/R/ranking.R
@@ -51,8 +51,8 @@ ranking <- function(analysis, weights) {
 #' @param analysis Results from [analyze()] or [ranking()].
 #' @param methods Methods to include in the score.
 #' @param reference_gene_ids IDs of the reference genes.
-#' @param target The optimization target. It may be one of "mean", "min" or
-#'   "max" and results in the respective rank being optimized.
+#' @param target The optimization target. It may be one of "mean", "median",
+#'   "min" or "max" and results in the respective rank being optimized.
 #'
 #' @returns Named list pairing method names with their optimal weights. This
 #'   can be used as an argument to [ranking()].
@@ -72,8 +72,10 @@ optimal_weights <- function(analysis, methods, reference_gene_ids,
             min(rank)
         } else if (target == "max") {
             max(rank)
-        } else {
+        } else if (target == "mean") {
             mean(rank)
+        } else {
+            median(rank)
         }]
 
         if (result > 0) {