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 user interface (GUI) for R that works under Windows, Linux, and Mac.
Thanks to Kylee for pointing out this frightening trend from the U.K. Border Agency. http://www.sciencemag.org/cgi/content/full/326/5949/30Essentially, the United Kingdom is experimenting with using mitochondrial and Y-chromosome markers to determine if asylum-seekers that flee persecution are actually from the nation in question. Advocates of this policy don't seem to understand that genetic variation is not nation-specific.
Dan Vorhaus and Lawrence Moore recently put together this excellent three part series on Genomics Law Report. Headlines about deCODE Genetics on the brink of insolvency and major shifts in the upper management of 23andMe inspired this series of posts on what would happen when a direct-to-consumer (DTC) genomics company goes declares bankruptcy.
Genome Browsers are nothing new, but JBrowse is a new JavaScript based genome browser that uses information from the UCSC genome browser and has the look and feel of Google Maps. It's extremely easy to zoom in and out and scroll around because all the "work" is being done by your computer rather than some server farm thousands of miles away.
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 clicky-box options in Stata's graphics editor. I want something that just looks nice, using the out-of-the-box defaults.
There were only a couple of citations for articles discussed at this week's PCG meeting (September 11). Our next meeting is scheduled for September 26.~JuliaKim S, Xing EP. Statistical estimation of correlated genome associations to a quantitative trait network. PLoS Genet. 2009 Aug; 5(8):e1000587.Zamar D, Tripp B, Ellis G, Daley D. Path: a tool to failitate pathway-based genetic association analysis. Bioinformatics. 2009 Sep 15;
At this week's R clinic Frank Harrell will unveil the new rms (Regression Modeling Strategies) package that is a replacement for the R Design package. He will demonstrate the differences with Design, especially related to enhanced graphics for displaying effects in regression models. Frank will also discuss the implementation of quantile regression in rms.
Any R user no matter what level of experience has had trouble finding the package or the function to do what you want to do and then figuring out how to use it. The sos package in R just made that a lot easier. First, fire up R, then install the sos package (don't omit the quotes): install.packages("sos") It'll ask you to choose a mirror. Choose the closest one.
Revolutions blog recently posted a link to R code by Joshua Reich with self-contained examples of using machine learning techniques in R, including various clustering methods (k-means, nearest neighbor, and kernel), recursive partitioning (CART), principle components analysis, linear discriminant analysis, and support vector machines. This post also links to some slides that go over the basics of machine learning.
Vanderbilt ACCRE users with PCs only... If you use ACCRE to run multi-processor jobs you'll be glad to know that they now allow you to map your home directory to your local desktop using Samba (so you can access your files through My Computer as you normally would with local files).
In the last post I showed you how to point to a file in windows and get the full path copied to your clipboard. I wanted to come up with something similar for a Linux environment. This is helpful on Vampire/ACCRE because you have to fully qualify the path to every file you use when you submit jobs with PBS scripts.