From 044966d72fc58d8234d0a5837c6744cb48a136f5 Mon Sep 17 00:00:00 2001
From: Helen Laboe <hlaboe@nd.edu>
Date: Mon, 15 Nov 2021 18:26:56 -0500
Subject: [PATCH 1/5] Getting started on Exercise09

---
 Exercise09.R | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 Exercise09.R

diff --git a/Exercise09.R b/Exercise09.R
new file mode 100644
index 0000000..dae7c06
--- /dev/null
+++ b/Exercise09.R
@@ -0,0 +1,13 @@
+### Biocomputing Exercise09 - Pulling the R pieces together
+
+# Create the coefficient of variation vector
+coefficientofvariationVector = vector(mode="numeric", 0)
+
+# Set a working directory 
+setwd(dir)
+inputfiles<-list.files(dir)
+
+# Sets up a loop for the files in the directory to calculate the coefficient of variation
+for (file in inputfiles){
+  file<- read.table(file, header=TRUE, sep=",", stringsAsFactors = FALSE)
+}
\ No newline at end of file

From a4f0944d9bf08155824a0bd050ad579b7e95fb5b Mon Sep 17 00:00:00 2001
From: Helen Laboe <hlaboe@nd.edu>
Date: Wed, 17 Nov 2021 22:41:36 -0500
Subject: [PATCH 2/5] Script for Exercise09

---
 Exercise09.R | 44 +++++++++++++++++++++++++++++++++++---------
 1 file changed, 35 insertions(+), 9 deletions(-)

diff --git a/Exercise09.R b/Exercise09.R
index dae7c06..2de94ea 100644
--- a/Exercise09.R
+++ b/Exercise09.R
@@ -1,13 +1,39 @@
 ### Biocomputing Exercise09 - Pulling the R pieces together
 
-# Create the coefficient of variation vector
-coefficientofvariationVector = vector(mode="numeric", 0)
+# Defining the function
+CoefficientofVariation <- function(dir,col,nrow=50){
+  
+  # Set a working directory and create the Coefficient of Variation vector
+  setwd(dir)
+  inputfiles<-list.files(dir)
+  coefficientofvariationVector <- numeric(0)
+  
+  # Sets up a loop for the files in the directory to calculate the coefficient of variation
+  for (i in inputfiles){
+    i <- read.csv(i,header=TRUE,sep=",",stringsAsFactors=FALSE, fill=TRUE)
+    if(ncol(i)< col){
+      print("Invalid column number.")
+    }else{
+      if(nrow(i) <50){
+        not50 <- print("Recommended that the file has at least 50 observations to calculate a coefficient of variation. Would you like to proceed? Type 'Y' for Yes and 'N' for No: ")
+        if(not50=="Y"){
+          mean=mean(i[,col])
+          standarddeviation=sd(i[,col])
+          coefficientofvariation=standarddeviation/mean
+          coefficientofvariationVector=c(coefficientofvariationVector,coefficientofvariation)
+        }else{
+          print("Function stopped.")
+        }
+      }else{
+        mean=mean(i[,col])
+        standardeviation=sd(i[,col])
+        coefficientofvariation=standardeviation/mean
+        coefficientofvariationVector=c(coefficientofvariationVector,coefficientofvariation)
+      }
+    }
+  }
+  
+  return(coefficientofvariationVector)
+}
 
-# Set a working directory 
-setwd(dir)
-inputfiles<-list.files(dir)
 
-# Sets up a loop for the files in the directory to calculate the coefficient of variation
-for (file in inputfiles){
-  file<- read.table(file, header=TRUE, sep=",", stringsAsFactors = FALSE)
-}
\ No newline at end of file

From 16d16603db332c1a09804e58e74a5b3ab19ea690 Mon Sep 17 00:00:00 2001
From: hlaboe <91484525+hlaboe@users.noreply.github.com>
Date: Wed, 17 Nov 2021 22:46:28 -0500
Subject: [PATCH 3/5] Delete Exercise09.R

---
 Exercise09.R | 39 ---------------------------------------
 1 file changed, 39 deletions(-)
 delete mode 100644 Exercise09.R

diff --git a/Exercise09.R b/Exercise09.R
deleted file mode 100644
index 2de94ea..0000000
--- a/Exercise09.R
+++ /dev/null
@@ -1,39 +0,0 @@
-### Biocomputing Exercise09 - Pulling the R pieces together
-
-# Defining the function
-CoefficientofVariation <- function(dir,col,nrow=50){
-  
-  # Set a working directory and create the Coefficient of Variation vector
-  setwd(dir)
-  inputfiles<-list.files(dir)
-  coefficientofvariationVector <- numeric(0)
-  
-  # Sets up a loop for the files in the directory to calculate the coefficient of variation
-  for (i in inputfiles){
-    i <- read.csv(i,header=TRUE,sep=",",stringsAsFactors=FALSE, fill=TRUE)
-    if(ncol(i)< col){
-      print("Invalid column number.")
-    }else{
-      if(nrow(i) <50){
-        not50 <- print("Recommended that the file has at least 50 observations to calculate a coefficient of variation. Would you like to proceed? Type 'Y' for Yes and 'N' for No: ")
-        if(not50=="Y"){
-          mean=mean(i[,col])
-          standarddeviation=sd(i[,col])
-          coefficientofvariation=standarddeviation/mean
-          coefficientofvariationVector=c(coefficientofvariationVector,coefficientofvariation)
-        }else{
-          print("Function stopped.")
-        }
-      }else{
-        mean=mean(i[,col])
-        standardeviation=sd(i[,col])
-        coefficientofvariation=standardeviation/mean
-        coefficientofvariationVector=c(coefficientofvariationVector,coefficientofvariation)
-      }
-    }
-  }
-  
-  return(coefficientofvariationVector)
-}
-
-

From e565db539b75e77c1f107917102c9d62f141a930 Mon Sep 17 00:00:00 2001
From: Helen Laboe <hlaboe@nd.edu>
Date: Wed, 17 Nov 2021 22:48:01 -0500
Subject: [PATCH 4/5] This is the script for Exercise09

---
 Exercise09.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/Exercise09.R b/Exercise09.R
index 2de94ea..34e4686 100644
--- a/Exercise09.R
+++ b/Exercise09.R
@@ -2,8 +2,8 @@
 
 # Defining the function
 CoefficientofVariation <- function(dir,col,nrow=50){
-  
-  # Set a working directory and create the Coefficient of Variation vector
+ 
+   # Set a working directory and create the Coefficient of Variation vector
   setwd(dir)
   inputfiles<-list.files(dir)
   coefficientofvariationVector <- numeric(0)
@@ -35,5 +35,7 @@ CoefficientofVariation <- function(dir,col,nrow=50){
   
   return(coefficientofvariationVector)
 }
+  
+
 
 

From f655427130b64dd910e088d40b4f75f149a5b6e2 Mon Sep 17 00:00:00 2001
From: Helen Laboe <hlaboe@nd.edu>
Date: Wed, 17 Nov 2021 22:57:24 -0500
Subject: [PATCH 5/5] Adding commentary

---
 Exercise09.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/Exercise09.R b/Exercise09.R
index 34e4686..51b638e 100644
--- a/Exercise09.R
+++ b/Exercise09.R
@@ -11,10 +11,13 @@ CoefficientofVariation <- function(dir,col,nrow=50){
   # Sets up a loop for the files in the directory to calculate the coefficient of variation
   for (i in inputfiles){
     i <- read.csv(i,header=TRUE,sep=",",stringsAsFactors=FALSE, fill=TRUE)
+    # Checking if the file has the correct number of columns
     if(ncol(i)< col){
       print("Invalid column number.")
     }else{
+      # Checking if the column has 50 observations
       if(nrow(i) <50){
+        # Offers the override option if the column does not have 50 observations
         not50 <- print("Recommended that the file has at least 50 observations to calculate a coefficient of variation. Would you like to proceed? Type 'Y' for Yes and 'N' for No: ")
         if(not50=="Y"){
           mean=mean(i[,col])
@@ -22,6 +25,7 @@ CoefficientofVariation <- function(dir,col,nrow=50){
           coefficientofvariation=standarddeviation/mean
           coefficientofvariationVector=c(coefficientofvariationVector,coefficientofvariation)
         }else{
+          # Output if the user chooses not to override
           print("Function stopped.")
         }
       }else{