correlation: Score based on best correlation

R/correlation.R

@@ -1,5 +1,4 @@
-#' Compute the mean correlation coefficient comparing gene distances with a set
+#' Score genes based on their correlation with the reference genes.
-#' of reference genes.
 #'
 #' @return An object of class `geposan_method`.
 #'
@@ -66,28 +65,21 @@ correlation <- function() {
 
                     progress(0.66)
 
-                    # Compute the final score as the mean of known correlation
+                    # Find the highes correlation.
-                    # scores. Negative correlations will correctly lessen the
-                    # score, which will be clamped to zero as its lower bound.
-                    # Genes with no possible correlations at all will be assumed
-                    # to have a score of 0.0.
-
-                    compute_score <- function(scores) {
-                        score <- mean(scores, na.rm = TRUE)
-
-                        if (is.na(score) | score < 0.0) {
-                            score <- 0.0
-                        }
-
-                        score
-                    }
-
                     results[,
-                        score := compute_score(as.matrix(.SD)),
+                        max_correlation := max(.SD, na.rm = TRUE),
                         .SDcols = reference_gene_ids,
                         by = gene
                     ]
 
+                    # Normalize scores.
+                    results[,
+                        score := (max_correlation - min(max_correlation)) /
+                            (max(max_correlation) - min(max_correlation))
+                    ]
+
+                    # Normalize scores.
+
                     results[, .(gene, score)]
 
                     result(

man/correlation.Rd

@@ -2,8 +2,7 @@
 % Please edit documentation in R/correlation.R
 \name{correlation}
 \alias{correlation}
-\title{Compute the mean correlation coefficient comparing gene distances with a set
+\title{Score genes based on their correlation with the reference genes.}
-of reference genes.}
 \usage{
 correlation()
 }
@@ -11,6 +10,5 @@ correlation()
 An object of class \code{geposan_method}.
 }
 \description{
-Compute the mean correlation coefficient comparing gene distances with a set
+Score genes based on their correlation with the reference genes.
-of reference genes.
 }