The first post on Getting Genetics Done was one year ago today. To celebrate, here are the top 10 most viewed posts since GGD launched last year. Incidentally, nine of the ten are tutorials on how to do something in R. Thanks to all the readers and all... [Read more...]

Department of Biostatistics Seminar/Workshop Series: Statistical Methods for DNA Resequencing Analysis in Disease-Gene Studies Wenyi Wang, Ph.D., Faculty Candidate Stanford Genome Technology Center, UC Berkeley Statistics 2:00-3:00pm Monday, Februa... [Read more...]

Update Friday, May 14, 2010: See this newer post on LocusZoom. If you caught Cristen Willer's seminar here a few weeks ago you saw several beautiful figures in the style of a manhattan plot, but zoomed in around a region of interest, with several ot... [Read more...]

Frank Harrell is teaching his 3-session short course on regression modeling strategies using R here at Vanderbilt next month. Frank is a professor and chair of the Vanderbilt Biostatistics Department, and the author of several massively popular R libra... [Read more...]

Found this nice way to visually summarize contingency tables using ggplot2 in R on Hadley Wickham's ggplot2 cheat sheet. Using the same data in my previous post on making scatterplots in small multiples, I'll demonstrate how to use ggfluctuation() to m... [Read more...]

Will posted earlier this week about how to produce manhattan plots of GWAS results using Stata, so I thought I'd share how I do this in R using ggplot2. First, if you've never used ggplot2, you'll need to add it to your R installation by typing: install.packages("ggplot2") Once ... [Read more...]

Head over to Revolutions Blog for a list of PDF and powerpoint resources for making the transition to R from other programming or stats languages.  All of these notes come from the New York R meetup. I enjoyed browsing the meetup's files - lots of powerpoints, PDFs, and example R ... [Read more...]

It took several months after learning about ggplot2 before I gave it a try myself.  I was apprehensive about learning a new graphics system with a new set of commands.  Thing is, if you've ever used plot() in R, you already know how to use much of the functionality in ... [Read more...]

Learning R blog details some of the new features in the latest update to ggplot2. The latest version includes functions to make it easier to change axis and legend labels, as well as a function to easily set the limits of the plot display outside the range of the data. ... [Read more...]

I've covered plyr once before, showing you how to get means and variances for two quantitative traits across multilocus genotypes. JD Long over at Cerebral Mastication recently posted a nice screencast illustrating how plyr "just works" as an alternative to R's family of apply commands.  There's a set of R ... [Read more...]

Just discovered this very handy R command to capture the output from a system command as an R object.  I wanted to use R to read in the output from another program (PLINK) and do some processing on each output file. Of course if the files are named sequentially (plink1.... [Read more...]

One of R's biggest strengths is its unparalleled graphing capabilities.  Just see any of our previous posts on ggplot2, visualization, or other posts tagged with R. R has several fundamentally different systems for plotting, including base graphics, lattice, and ggplot2.  Furthermore, many add-on packages come with their own functions for ... [Read more...]

A Beautiful WWW put together a great set of resources for getting started with machine learning in R.  First, they recommend the previously mentioned free book, The Elements of Statistical Learning.  Then there's a link to a list of dozens of machine learning and statistical learning packages for R.  Next, ... [Read more...]

The New York Times had an interesting piece yesterday about how SAS is facing several business threats from companies like the recently IBM-acquired SPSS, and from burgeoning interest in open-source software like R.  The NYT ran an entire article about R earlier this year, and this article discusses how SAS ... [Read more...]

Theresa Scott, instructor of the previously mentioned R workshop and weekly R clinic, is giving a lecture entitled "Reproducible Research with R, LaTeX, & Sweave" in MRB III, room 1220, this Wednesday 11/18 at 1:30.  You can see more details about the lecture here. Looks like her slides as well as much more introductory ... [Read more...]

Way back will wrote on this topic.  See his previous post for Stata code for doing this.  Unfortunately the R package that was used to create QQ-plots here has been removed from CRAN, so I wrote my own using ggplot2 and some code I received from Daniel Shriner at NHGRI. ... [Read more...]

While flirting around with previously mentioned ggplot2 I came across an incredibly useful set of functions in the plyr package, made by Hadley Wickham, the same guy behind ggplot2.  If you've ever used MySQL before, think of "GROUP BY", but here you can arbitrarily apply any R function to splits ... [Read more...]

Strict quality control procedures are extremely important for any genome-wide association study.  One of the first steps you should take when running QC on your GWAS is to look for related samples in your dataset.  This does two things for you.  First, you can get an idea of how many ... [Read more...]

R is a great tool with lots of resources for genetics, genome-wide association studies, and many other biological applications.  We've covered several places to find help in R in the past, but if you're still apprehensive about diving into R's command-line interface, fear not.  The R commander is a graphical ... [Read more...]

One of the nicer things about many statistics packages is the extremely granular control you get over your graphical output.  But I lack the patience to set dozens of command line flags in R, and I'd rather not power the computer by pumping the mouse trying to set all the ... [Read more...]