SynergyScreen is an R package that I have developed to facilitate design and analysis of medium-throughput compound synergy screens using single-ray design. These slides describe the functionality of the package and R programming techniques. These slides were presented at Madison R Meet-up (MadR) on 18 January 2017.

1. The SynergyScreen Package
Yury V Bukhman
MadR Meetup, 18 January 2017

2. Overview
Scientific background
SynergyScreen functionality
Using S4 classes
Developing a package
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3. Scientific Background
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4. How to Make Biofuels
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HydrolysateBiomass
Microbes
Fuel
Problem: hydrolysate
contains compounds
that are toxic to
microbes

5. What is Synergy?
Synergy is “the interaction or cooperation of
two or more organizations, substances, or
other agents to produce a combined effect
greater than the sum of their separate
effects” (Google)
Synergy is when the effect of two toxins is
greater than expected when they do not
interact
The opposite of synergy is called antagonism
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6. The Isobole Method
Interaction Index: 𝐼 =
𝑑 𝐴
𝐷 𝐴
+
𝑑 𝐵
𝐷 𝐵
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No interaction: I = 1 Synergy: I < 1 Antagonism: I > 1

7. Single Ray Experimental
Design
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8. Dose-Response Curve
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Median effect equation:

9. Experiments in Microtiter
Plates
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10. 96 Well Plate Layouts
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11. SynergyScreen Functionality
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12. SynergyScreen Workflow
Input: a set of compounds and dose ranges
Generate experimental design
[A wet lab scientist conducts the experiment]
Read in experimental results
Compute
 Normalize data from multiple plates
 Model dose-response curves
 Compute interaction index values
Find synergies and antagonisms
Plot results
 Interaction matrix
 Isoboles
 Dose-response curves
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13. SynergyScreen Commands
See quick start vignette
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14. Using S4 Classes
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15. S4 Classes
Why use classes? As opposed to (nested) lists and data
frames?
 Constrain and validate contents of objects
 Define custom show, plot and other methods
 Inheritance
[At least] 3 OOP systems in R: S3, S4 and RC
S4 is recommended by Bioconductor project
S4 learning resources
 Hadley Wickham, Advanced R, OO field guide, S4: http://adv-
r.had.co.nz/OO-essentials.html#s4
 John Chambers’ Software for Data Analysis
 S4 system development in Bioconductor
 My S4 slides: http://rpubs.com/ybukhman/intro_to_S4
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16. Synergy Screen Structure
Synergy screen
 Compounds
 Experimental design
 Raw data
 Normalized data
 Dose-response experiments
• Compounds; doses; responses; models
 Synergy experiments
• Dose-response experiments
 Interaction index values
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17. Define an S4 class
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18. Slot accessors
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Define generic functions
Define methods

19. Auto-generate accessors
Use function standardMethods from
package distr.
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20. Custom plot method
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Generic plot function supplied by R: plot(x, y, …)

21. Debug a method
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I know this is a hack. However, in my hands, setting break points in
Rstudio or using trace() did not consistently work.

22. An S4 class that extends list
How: use contains argument with setClass
Why: constrain list elements, e.g. to be of the same
class, DRE
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setClass("DREList", contains="list",
validity=function(object) {
checks = sapply(object, is, "DRE")
if(!all(checks)) {
return(paste("The following elements are not of class DRE:",
paste(object[!checks], collapse="; ")))
}
# Check names
cnames = sapply(object, function(x) x@name)
if (is.null(names(object)) || any(names(object) != cnames){
return("Inconsistent names")
}
# All done
return(TRUE)
}
)

23. Coerce list to S4 class
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24. Developing a Package
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25. Why develop a package?
Users can download and install your software
using standard procedures
Provide documentation for your software
Provide example dataset(s)
Submit your code to CRAN or Bioconductor
Publish a paper
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26. Initialize a new R package
Create a new package from an R session:
devtools::create(“MyNewPackage”)
Initialize a project at a git or SVN server
Edit DESCRIPTION
Let roxygen2 generate and manage NAMESPACE
Add a package documentation file, e.g. MyNewPackage.R
Start writing a vignette:
devtools::use_vignette(“my-first-
vignette”)
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27. DESCRIPTION
Information about your package and its
maintainer
License
List of other packages that your package
needs to function
Information on how to collate files in your
package (autogenerated by roxygen2)
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28. Package structure
Project root folder: DESCRIPTION, NAMESPACE,
.gitignore, .Rbuildignore, RStudio project file
(SynergyScreen.Rproj)
Subfolders
 R – .R files that contain functions, classes, methods etc.
 man – help pages (.Rd)
 data - datasets
 tests – test scripts
 vignettes – long-form documentation using R markdown
 inst – other stuff, e.g. raw data files, one-off scripts etc.
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29. Document your package
Use roxygen2 to parse specially formatted
comments and generate documentation (.Rd)
files
Write long form documentation in the form
of vignettes
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30. Package documentation file
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31. Document a class
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32. Document a method
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[….]

33. Document accessor methods
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34. Document accessor methods
continued
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35. Document a dataset
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36. Organize code and
documentation files
Organize by generic function
Organize by class
Use @include tags to specify collation
order
Put data documentation in data.R
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37. Namespace
Why namespaces?
 Avoid confusion when different packages define functions that have
the same name
 Import functions from other packages
 Export functions from your package to make them accessible to others
Poor practice
 Edit file NAMESPACE manually
 Export everything
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38. Good Practice
Read Hadley’s book, http://r-
pkgs.had.co.nz/namespace.html
Let roxygen2 generate the NAMESPACE file
For imports:
 List packages under Imports field in DESCRIPTION
 Call functions explicitly by package::function
 For frequently used functions, use @importFrom package
function
 To import all functions from a package, use @import package
For exports:
 use the @export tag to export functions, classes and methods
 Datasets are exported automatically: no need for @export
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39. A NAMESPACE file generated
by roxygen2
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40. Tests
Why test? Verify that new edits do not inadvertently damage
previously developed functionality.
Use package testthat. Read Hadley’s book: http://r-
pkgs.had.co.nz/tests.html
Do a package check or just run the tests. The former also
checks syntax, documentation etc.
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41. Questions?
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