From 707d8d0f958c7363d47c8b7d2371ec243c0eaf65 Mon Sep 17 00:00:00 2001
From: tew42 <2049715+tew42@users.noreply.github.com>
Date: Tue, 16 Feb 2021 15:26:04 +0100
Subject: [PATCH 1/3] Update statAnalysis.R

allow negative values
---
 R/statAnalysis.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/statAnalysis.R b/R/statAnalysis.R
index 1f78fca..7cbe77f 100755
--- a/R/statAnalysis.R
+++ b/R/statAnalysis.R
@@ -68,9 +68,9 @@ statAnalysis <- function(file, Frule = 0.8, normM = "NONE", imputeM = "KNN", glo
     
     imdat <- dat[, 3:ncol(dat)]
     
-    if (length(imdat[imdat < 0L]) > 0) {
-        imdat[imdat < 0L] <- 0L
-    }
+    #if (length(imdat[imdat < 0L]) > 0) {
+    #    imdat[imdat < 0L] <- 0L
+    #}
     imdat[imdat == 0L] <- NA
     
     imdat <- cbind(dat[, 1:2], imdat)

From 186eb6f407f1dffaf6c1132dcd1f11f4bddbab60 Mon Sep 17 00:00:00 2001
From: tew42 <2049715+tew42@users.noreply.github.com>
Date: Thu, 4 Mar 2021 23:18:39 +0100
Subject: [PATCH 2/3] Update statAnalysis.R

---
 R/statAnalysis.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/statAnalysis.R b/R/statAnalysis.R
index 7cbe77f..1f78fca 100755
--- a/R/statAnalysis.R
+++ b/R/statAnalysis.R
@@ -68,9 +68,9 @@ statAnalysis <- function(file, Frule = 0.8, normM = "NONE", imputeM = "KNN", glo
     
     imdat <- dat[, 3:ncol(dat)]
     
-    #if (length(imdat[imdat < 0L]) > 0) {
-    #    imdat[imdat < 0L] <- 0L
-    #}
+    if (length(imdat[imdat < 0L]) > 0) {
+        imdat[imdat < 0L] <- 0L
+    }
     imdat[imdat == 0L] <- NA
     
     imdat <- cbind(dat[, 1:2], imdat)

From a27ed642061449487414aee32434f8bdf5b7fb7f Mon Sep 17 00:00:00 2001
From: tew42 <2049715+tew42@users.noreply.github.com>
Date: Thu, 4 Mar 2021 23:19:30 +0100
Subject: [PATCH 3/3] Update shapiro.R

---
 R/shapiro.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/shapiro.R b/R/shapiro.R
index b74b425..bab5c28 100755
--- a/R/shapiro.R
+++ b/R/shapiro.R
@@ -45,11 +45,11 @@ shapiro <- function(file) {
         shapiro = matrix(rep(NA, ncol(n.x)))
         for (q in 1:ncol(name)) {
             notAlist = c()
-            notAlist = matrix(unlist(name[, q]))
+            notAlist = as.numeric(matrix(unlist(name[, q])))
             if (diff(range(notAlist)) == 0) {
                 shapiro[q, ] = NA
             } else {
-                shapiro[q, ] = shapiro.test(as.numeric(notAlist))$p.value
+                shapiro[q, ] = shapiro.test(notAlist)$p.value
             }
             assign(shapname, shapiro)
         }