Often when presenting statistics from a candidate gene study, or a region of interest from a genome-wide association study, it is useful to see various SNP-wise values in the context of linkage disequilibrium patterns.
Aloha! If you're going to the American Society of Human Genetics meeting next week, come by our poster (poster #116, abstract #1567/T) and say hello! We would love to meet any of you who read GGD and hear what you think and what you'd like to see in the future.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
The Elements of Statistical Learning: Data Mining, Inference, and Prediction by Trevor Hastie, Robert Tibshirani, and Jerome Friedman, one of the best books on data mining and machine learning, is now available free in PDF format. Download it here or view it online here.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
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.
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.