diff Intchecks/Script_intensity_check.R @ 6:ec75de7f1e08 draft default tip

Uploaded

--- a/Intchecks/Script_intensity_check.R	Wed Jan 22 09:34:08 2020 -0500
+++ b/Intchecks/Script_intensity_check.R	Mon Dec 11 12:56:20 2023 +0000
@@ -20,7 +20,7 @@
   VM.name <- "vM_NA.tabular"
   method <- "one_class"
   chosen.stat <- "mean,sd,quartile,decile,NA" 
-  class.col <- "2" 
+  class.col <- "uv" 
   test.fold <- "Yes" 
   class1 <- "Pools"
   fold.frac <- "Top"
@@ -97,11 +97,9 @@
 
 
   if(method != "no_class"){
-    
-    class.col <- colnames(SM)[as.numeric(class.col)]
   
     if(!(class.col %in% colnames(SM))){
-      stop("\n- - - - - - - - -\n", "The column ",class.col, " is not a part of the specify sample Metadata","\n- - - - - - - - -\n")
+      stop("\n- - - - - - - - -\n", "The ",class.col, " column is not found in the specified sample metadata file.","\n- - - - - - - - -\n")
     }
   
     c_class <- SM[,class.col]
@@ -110,7 +108,7 @@
     classnames <- levels(c_class)
   
     if((nb_class < 2)&&(test.fold=="Yes")){
-      err.1class <- c("\n The column",class.col, "contains only one class, fold calculation could not be executed. \n")
+      err.1class <- c("\n The ",class.col, " column contains only one class, fold calculation could not be executed. \n")
       cat(err.1class)  
     }
   
@@ -125,7 +123,7 @@
       if(!(class1 %in% classnames)){
         list.class1 <- c("\n Classes:",classnames,"\n")
         cat(list.class1)
-        err.class1 <- c("The class ",class1, " does not appear in the column ", class.col)
+        err.class1 <- c("The ",class1, " class does not appear in the ",class.col," column.")
         stop("\n- - - - - - - - -\n", err.class1,"\n- - - - - - - - -\n")
       }