Hansong Wang, our biostats professor here at the Hawaii Cancer Center, generously gave me some R code that goes through a SNP annotation file (i.e. a mapfile) and selects SNPs that are at least a certain specified distance apart. You might want to do this if you're picking a subset of SNPs for PCA, for instance.

I recently started using RStudio, the amazing new IDE for R. You can view all of RStudio's keyboard shortcuts by going to the help menu, but I made this printable reference for myself and thought I'd share it. I only included the Windows shortcuts, and I cut out all the obvious ones (Ctrl-S for save, Ctrl-O for open, etc) so it would fit neatly on one page.

The *ABEL suite of R packages and software for genetic analysis has grown substantially since the appearance of GenABEL and the previously mentioned ProbABEL R packages. There are now a handful of useful R packages and other software utilities facilitating genome-wide association studies, analysis of imputed data, meta-analysis, efficient data storage, prediction, parallelization, and mixed model methods.

Thanks to links from Sarah Pendergrass, I stumbled upon this awesome program for graph visualization and analysis called Gephi. It seems rather feature rich, with built in connectors to database systems, extensive graph coloring, layout, and rendering features, and several analysis tools.

Abhijit over at Stat Bandit posted some nice code for making forest plots using ggplot2 in R. You see these lots of times in meta-analyses, or as seen in the BioVU demonstration paper. The idea is simple - on the x-axis you have the odds ratio (or whatever stat you want to show), and each line is a different study, gene, SNP, phenotype, etc.

In my previous post I showed you how to randomly split up a dataset into training and testing datasets. (Thanks to all those who emailed me or left comments letting me know that this could be done using other means.

Genetic Alliance is a nonprofit health advocacy organization that improves health through the authentic engagement of communities and individuals. This year, they are celebrating their 25th anniversary, and they're hosting a variety of events throughout the year, including monthly salons around the country and the 25th Anniversary Annual Conference in June.

Just saw the announcement of the availability of Rstudio, a new (free & open source) integrated development environment for R that works on Windows, Mac, and Linux. Judging from the screenshots, it looks like Rstudio supports syntax highlighting for Sweave &

I recently analyzed some data trying to find a model that would explain body fat distribution as predicted by several blood biomarkers. I had more predictors than samples (p>n), and I didn't have a clue which variables, interactions, or quadratic terms made biological sense to put into a model.

When I have a question I usually ask the internet before bugging my neighbor.