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A few months ago I covered an algorithm called EMMA (Efficient Mixed-Model Association) implemented in R for simultaneously correct for both population stratification and relatedness in an association study. This method/software is very useful because ... [Read more...]

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...]

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...]

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...]

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...]