If you caught Soumya Raychaudhuri's seminar last week you heard a lot about the tool he developed at the broad called GRAIL - Gene Relationships Across Implicated Loci. You've got GWAS results and now you want to prioritize SNPs to follow up in replication or functional studies.

"The hunt for the genetic roots of common diseases has hit a blank wall." ...quoting the first sentence in Nicholas Wade's New York Times article reviewing this PLoS Biology research paper by David Goldstein and his colleagues at Duke University. Also be sure to see Richard Robinson's synopsis of this paper, both published this week in PLoS Bio.

Soumya Raychaudhuri is the lead author on the GRAIL paper in Nature Genetics. GRAIL (Gene Relationships Across Implicated Loci) is software available from the Broad Institute and looks like an interesting way to prioritize SNPs for followup. I'll cover it here in the future, but in the meantime, check out this seminar this Wednesday.

Found this nice way to visually summarize contingency tables using ggplot2 in R on Hadley Wickham's ggplot2 cheat sheet. Using the same data in my previous post on making scatterplots in small multiples, I'll demonstrate how to use ggfluctuation() to make a fluctuation plot.

**** UPDATE, May 15 2014 ***** The functions described here have now been wrapped into an R package. View the updated blog post or see the online package vignette for how to install and use. If you'd still like to use the old code described here, you can access this at version 0.0.0 on GitHub.

Christen J. Willer, (of the Willer et al Nature Genetics lipid genetics paper), postdoc at University of Michigan and departmental Faculty Candidate, will be giving a talk tomorrow (Wednesday Jan 20) at noon in 208 Light Hall. I'll be going to this one. Topic:

I have used this chunk of code on numerous occasions to plot GWAS data, so I thought I'd share! The variables needed are a log p-value (or some other statistic) and the absolute genomic position of each SNP (distance from the beginning of chromosome 1). If you need the offsets to compute this absolute position, they are listed in MB in the xline(---) portion of the plot.

Head over to Revolutions Blog for a list of PDF and powerpoint resources for making the transition to R from other programming or stats languages.  All of these notes come from the New York R meetup. I enjoyed browsing the meetup's files - lots of powerpoints, PDFs, and example R data files for various topics, including several slideshows on ggplot2.

Do you submit manuscripts to journals that are not indexed in PubMed? This can make it difficult for others to find your publications, especially if they don't have a subscription to the journal. This often happens with us when we publish in computer science journals. Using the NIH manuscript submission system you can upload your manuscript to PubMed Central, which provides free open access, and is indexed in PubMed.

Illumina just unveiled their latest sequencing machine, the HiSeq 2000, capable of sequencing two human genomes to 30x coverage in a single run for less than $10,000 each. Using reversible terminator-based sequencing by synthesis chemistry, the HiSeq 2000 is capable of quickly generating a flood of data: 200 Gb per run, 2 x 100 bp read length, up to 25 Gb per day, two billion paired-end reads/run.

This looks good.  208 Light Hall Wednesday 1/13/2010, Noon Charles Rotimi Health Disparities in the Genomic Era: What are we Learning? Charles Rotimi, PhD, a genetic epidemiologist and a biochemist, is a senior investigator in the Inherited Disease Branch of the NHGRI intramural program.