Summer Institute in Statistical Genetics
Module 6: Elements of R for Genetics & Bioinformatics
Instructors: Thomas Lumley and Ken Rice
This page will feature slides from our sessions, exercises for you to complete, and their solutions (all to follow). Prior to the module, please install on an up-to-date version of R on the laptop you will use during the summer institute. R is free, and is available from this site.
To download and install Bioconductor to your laptop, first log on to the internet. Then open an R session and enter the following;
After doing this download, to download new Bioconductor packages (for example the hexbin package) use the following commands;
Slides and exercises
Script files are posted following each session; these will contain our R code for the exercises. To make them work on your computer, remember to modify file names and locations appropriately. Also note that many different 'correct' solutions are possible.
Session 1, Introductions, reading in data. Exercises [.doc .pdf] (R script file)
Session 2, Learning to Draw. Exercises [.doc .pdf] (R script file)
Session 3, More advanced graphics. Exercises [.doc .pdf] (R script file)
Session 4, Data Manipulation. Exercises [.doc .pdf] (R script file)
Session 5, Replication - simulation and permutation. Exercises [.doc .pdf] (R script file)
Session 6, Writing Big Loops. Exercises [.doc .pdf] [timing commands] (R script file)
Special Exercise: This is a more in-depth programming problem, for you to try on Thursday night; we'll discuss it in the final session. [.doc, .pdf]
Session 7, Working with Big Data. Exercises [.doc .pdf] (R script file)
Session 8, Bioconductor Intro and Annotation. Exercises [.doc .pdf] (R script file)
Session 9, Bioconductor II. Exercises [.doc .pdf] (R script file)
Session 10, Special Exercise review and Interfacing R. [No exercises for this session]
For easier searching, here are all the slides in one document (PDF).
Please complete the evalulation. You will need the username and password used to register. Upon completing the evaluation, you will automatically get a PDF certificate of participation, for the module.
Datasets - in alphabetical order
Before trying to read data into your R session, we recommend looking at it first, in a text editor. Is the data comma- or tab-delimited? Does it have a 'header' row containing variable names?
Send mail to: see Thomas or Ken in class
Last modified: 7/14/2013