***Update Monday, November 09, 2009: The sma package is no longer available on CRAN. See this updated post for making QQ-plots in R using ggplot2.*** Nearly everyone who has read a paper on a genome-wide association study should now be familiar with the QQ-plot.
As far as I know there are 3 different systems for producing figures in R: (1) base graphics, included with R, (2) the lattice package, and (3) ggplot2, one of the newer plotting systems which is, according to the creator Hadley Wickham, "based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and none of the bad parts.
Last week personal genomics giant 23andMe launched Research Revolution, a new project aiming to recruit 1000 study participants for each of ten complex diseases, including Migraines, Psoriasis, several cancers, and autoimmune diseases.
Yesterday President Barack Obama announced his intent to appoint former leader of the Human Genome Project, discoverer of delta-F508, and all around science rockstar Francis Collins as the director of the National Institutes of Health.In his statement, Obama noted: "The National Institutes of Health stands as a model when it comes to science and research.
Nice review on the genetics of quantitative traits with good figures and references published this morning in Nature Reviews Genetics. Abstract:The genetics of quantitative traits: challenges and prospects (NRG AOP)Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
There's no doubt that by now you've noticed that we're big fans of R around here.
Both useful and delicious, this two-by-two table pie by Sarah Lowry, Sarah McDougal (my 2nd cousin) and friends of the UW MPH program helps you get genetics done and satisfies the appetite! If only she could mail me the Odds Ratio...Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Bioinformatics is running a special issue on next generation sequencing, featuring lots of papers on alignment, assembly, Chip-Seq, RNA-Seq, and other related topics. This "virtual issue" will be continually updated as more developments are made. From the editors:Bioinformatics: Next generation sequencing issueGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Here are citations for the articles discussed at our most recent meeting (June 24). Our next meeting is scheduled for July 17.~JuliaChoi Y, Wijsman EM, Weir BS. Case-control association testing in the presence of unknown relationships. Genet Epidemiol . 2009 Mar 30. [Epub ahead of print]Gao X, Becker LC, Becker DM, Starmer JD, Province MA. Avoiding the high Bonferroni penalty in genome-wide association studies. Genet Epidemiol .
For readers at Vanderbilt: At yesterday's R course I found out that Theresa Scott in the Biostatistics department holds a weekly R clinic and encourages new R users who want to learn more to bring any questions about R, or even your own code and data. The R clinic is held weekly on Thursday from 2:00-3:00 in MCN.
Writing from the previously mentioned intro to R course at the Kennedy Center. If you couldn't make it you can download all the course materials from Theresa Scott's website, under the "Current Teaching Material" heading. Here is a direct link to the PDF for the overview materials that we're going over today, along with the R code from the examples in this guide.