From fb18bed6fd796335a092ceabfa9f232d8818850a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Tue, 26 Dec 2023 20:04:21 +0100
Subject: [PATCH] fix: use R-squared instead of Pearson correlation coefficient

Fixes #48
---
 DESCRIPTION             | 2 +-
 NEWS.md                 | 7 +++++++
 R/qc_positive_control.R | 2 +-
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 308cecf1..770c24d6 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: NACHO
 Title: NanoString Quality Control Dashboard
-Version: 2.0.5
+Version: 2.0.6
 Authors@R: 
     c(person(given = "Mickaël",
              family = "Canouil",
diff --git a/NEWS.md b/NEWS.md
index 9602f6d3..eefc5747 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+# NACHO 2.0.6
+
+## Fixes
+
+- In `R/qc_positive_control.R`,
+  - fix: use R-squared instead of Pearson correlation coefficient. ([#48](https://github.com/mcanouil/NACHO/issues/48))
+
 # NACHO 2.0.5
 
 ## Fixes
diff --git a/R/qc_positive_control.R b/R/qc_positive_control.R
index 9245ed3a..0f93b548 100755
--- a/R/qc_positive_control.R
+++ b/R/qc_positive_control.R
@@ -10,6 +10,6 @@
 qc_positive_control <- function(counts) {
   measured <- log2(counts[["Count"]])
   known <- log2(as.numeric(sub("^[^(]*\\((.*)\\)$", "\\1", counts[["Name"]]))) # plexset value: "32"
-  correlation <- stats::cor.test(known, measured)$estimate
+  correlation <- summary(stats::lm(measured ~ known))$r.squared
   unname(round(correlation, 5))
 }