Install files and folders

.Rprofile

@@ -0,0 +1,14 @@
+init <- function() {
+    source(".init.R")
+}
+
+cat("\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n")
+cat("    =================")
+cat("\n\n")
+cat("        WELCOME !\n")
+cat("\n")
+cat("  Type  'init()'  to begin\n\n")
+cat("\n")
+cat("    =================")
+cat("\n\n")
+

.gitignore

@@ -1,9 +1,12 @@
+# Miscellaneous
+.Ds_store
+
 # History files
 .Rhistory
 .Rapp.history
 
 # Session Data files
-.RData
+# .RData
 
 # Example code in package build process
 *-Ex.R
@@ -15,7 +18,7 @@
 /*.Rcheck/
 
 # RStudio files
-.Rproj.user/
+# .Rproj.user/
 
 # produced vignettes
 vignettes/*.html
@@ -31,3 +34,4 @@ vignettes/*.pdf
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
+.Rproj.user

.init.R

@@ -0,0 +1,15 @@
+# .init.R
+# Functions to initialize this collection of learning units
+# Boris Steipe
+# ====================================================================
+
+# Create a local copy of myScript.R if required, and not been done yet.
+if (! file.exists("myScript.R") && file.exists(".tmp.R")) {
+    file.copy(".tmp.R", "myScript.R")
+}
+
+source(".utilities.R")
+
+file.edit("ABC-units.R")
+
+# [End]

.tmp.R

@@ -0,0 +1,22 @@
+# myScript.R
+#
+# Write your notes and code experiments into this document. Save it
+# from time to time - however I recommend that you do not _commit_ 
+# your saved version.
+#
+# As long as you do not _commit_ this script to version control, 
+# you can _pull_ updated versions of the entire project from GitHub
+# by using the RStudio version control interface. However, once 
+# you _commit_ any file in your local version, RStudio will require
+# you to resolve conflicts before you can _pull_ updates.
+#
+# ====================================================================
+
+
+
+
+
+
+
+# [END]
+

.utilities.R

@@ -0,0 +1,44 @@
+# .utilities.R
+#
+# Miscellaneous R code to suppport the project
+#
+# Version: 1.0
+# Date:    2016 12
+# Author:  Boris Steipe
+#
+# V 1.0    First code
+#
+# ToDo:
+# Notes:
+#
+# ==============================================================================
+
+objectInfo <- function(x) {
+    # Function to combine various information items about R objects
+    #
+    # Input: an R object
+    # Value: none - prints information as side-effect
+
+    cat("object contents:")
+    print(x, digits = 22)  # print value at maximal precision
+
+    cat("\nstructure of object:\n")
+    str(x)
+
+    if (! is.list(x)) { # Don't use cat() if x is a list. cat() can't handle lists.
+        cat("\nmode:   ", mode(x), "\n")
+        cat("typeof: ", typeof(x), "\n")
+        cat("class:  ", class(x), "\n")
+    }
+
+    # if the object has attributes, print them too
+    if (! is.null(attributes(x))) {
+        cat("\nattributes:\n")
+        attributes(x)
+    }
+    # Done
+}
+
+
+
+# [END]

ABC-units.R

@@ -0,0 +1,84 @@
+# ABC-units.R
+#
+# Purpose: A Bioinformatics Course: R code for learning units
+#
+# Version: 0.
+#
+# Date:    2017  08  18
+# Author:  Boris Steipe (boris.steipe@utoronto.ca)
+#
+# V 0.1    First code
+#
+# TODO:
+#
+#
+# == HOW TO WORK WITH THIS FILE ================================================
+#
+#  Go through this script line by line to read and understand the
+#  code. Execute code by typing <cmd><enter>. When nothing is
+#  selected, that will execute the current line and move the cursor to
+#  the next line. You can also select more than one line, e.g. to
+#  execute a block of code, or less than one line, e.g. to execute
+#  only the core of a nested expression.
+#
+#  Edit code, as required, experiment with options, or just play.
+#  Especially play.
+#
+#  DO NOT simply source() this whole file!
+#
+#  If there are portions you don't understand, use R's help system,
+#  Google for an answer, or ask me. Don't continue if you don't
+#  understand what's going on. That's not how it works ...
+#
+#  Once you have typed and executed the function init(), you will find a file
+#  called myScript.R in the project directory.
+#
+#  Open it, you can place all of your code-experiments and notes into that
+#  file. This will be your "Lab Journal" for this session.
+#
+# ==============================================================================
+
+" Introduction:
+  ...
+"
+
+
+# ==============================================================================
+#        PART ONE: REVIEW
+# ==============================================================================
+
+
+
+
+# == SECTION ===================================================================
+
+
+# == Subsection
+
+# Continue ...
+
+
+
+
+
+
+
+
+# ==============================================================================
+#        APPENDIX: OUTLOOK
+# ==============================================================================
+"There are many more functions for ... that this tutorial did not cover. You should know about the following. Look up the function and write a short bit of example code that uses it:"
+
+?subset
+?sweep
+?with     # ... and within()
+
+"Then you should know about the following packages. Open the vignette and browse through it. You should know be able to come up with least one use-case where the package functions would be useful:
+
+   https://cran.r-project.org/web/packages/magrittr/
+"
+
+
+
+
+# [END]

ABC-units.Rproj

@@ -0,0 +1,16 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: XeLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes

functionTemplate.R

@@ -0,0 +1,33 @@
+# functionTemplate.R
+#
+# Purpose:  (General)
+#
+# ToDo:
+# Notes:
+#
+# ==============================================================================
+
+myFunction <- function(a, b=1) {
+	# Purpose:
+	#     Describe ...
+    # Version:
+    # Date:
+    # Author:
+    #
+    # Parameters:
+	#     a: ...
+	#     b: ...
+	# Value:
+	#     result: ...
+
+	# code ...
+
+	return(result)
+}
+
+
+# ====  TESTS  =================================================================
+# Enter your function tests here...
+
+
+# [END]

scriptTemplate.R

@@ -0,0 +1,68 @@
+# scriptTemplate.R
+#
+# Purpose:
+# Version:
+# Date:
+# Author:
+#
+# Input:
+# Output:
+# Dependencies:
+#
+# ToDo:
+# Notes:
+# 
+# ==============================================================================
+
+setwd("<your/project/directory>")
+
+# ====  PARAMETERS  ============================================================
+# Define and explain all parameters. No "magic numbers" in your code below.
+
+
+
+# ====  PACKAGES  ==============================================================
+# Load all required packages.
+
+if (!require(RUnit, quietly=TRUE)) {
+    install.packages("RUnit")
+    library(RUnit)
+}
+
+
+# ====  FUNCTIONS  =============================================================
+
+# Define functions or source external files
+source("<myUtilityFunctionsScript.R>")
+
+myFunction <- function(a, b=1) {
+	# Purpose:
+	#     Describe ...
+	# Parameters:
+	#     a: ...
+	#     b: ...
+	# Value:
+	#     result: ...
+	
+	# code ...
+	
+	return(result)
+}
+
+
+
+# ====  PROCESS  ===============================================================
+# Enter the step-by-step process of your project here. Strive to write your
+# code so that you can simply run this entire file and re-create all
+# intermediate results.
+
+
+
+
+
+
+# ====  TESTS  =================================================================
+# Enter your function tests here...
+
+
+# [END]

taskSolutions.R

@@ -0,0 +1,12 @@
+# taskSolutions.R
+#
+# Code for (some of) the workshop tasks
+
+
+
+
+
+
+
+# [END]
+