Monthly Archives: March 2010

Create annotated GWAS manhattan plots using ggplot2 in R

March 18, 2010
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A few months ago I showed you in this post how to use some code I wrote to produce manhattan plots in R using ggplot2. The qqman() function I described in the previous post actually calls another function, manhattan(), which has a few options you can s...

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Webinar: High-Performance Analytics with R and Microsoft HPC Server

March 18, 2010
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On April 14 I'll be giving a new webinar in partnership with Microsoft on High-Performance Computing with R. I'll be focusing on the new parallel programming capabilities of REvolution R Enterprise 3.1 for Windows, and how to use the features of Microsoft HPC Server to enable computing on clusters. Here's the complete agenda, and you can register at the...

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Course in San Antonio, Texas

March 18, 2010
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Course in San Antonio, Texas

Yesterday, I gave my short (3 hours) introduction to computational Bayesian statistics to a group of 25-30 highly motivated students. I managed to cover “only” the first three chapters, as I included some material on Bayes factor approximation and only barely reached Metropolis-Hastings. Here are the slides, modified from the original Bayesian Core slides: (It

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O’Reilly at OSBC: The future’s in the data

March 17, 2010
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Tim O'Reilly's keynote talk at OSBC this evening was thought-provoking to say the least. The title of the talk was "The Real Open Source Opportunity", and the surprise for me was that he wasn't talking about Open Source software. Tim's insight, and it's a profound one, is that the next frontier for freedom and openness -- and indeed, the...

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Tools

March 17, 2010
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Tools

All the tools I am using at the moment are free of charge. The one that comes to mind first is R. It’s a language for statistical computing which comes with a decent GUI. R comes with some time series support out of the box, but there are plenty of packages (R extensions are called

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Vanilla Rao-Blackwellisation for revision

March 17, 2010
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Vanilla Rao-Blackwellisation for revision

The vanilla Rao-Blackwellisation paper with Randal Douc that had been resubmitted to the Annals of Statistics is now back for a revision, with quite encouraging comments: The paper has been reviewed by two referees both of whom comment on the clear exposition and the novelty of the results. Both referees point to the empirical results

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OSBC blogging

March 17, 2010
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I'm at the Open Source Business Conference in San Francisco today and tomorrow; I'll report in with updates after the talks. I'm particularly looking forward to the panel discussion on The Shifting Open Source Opportunity moderated by Ashlee Vance, the New York Times reporter who wrote the major story on R last year. (Interesting aside: I learned recently that...

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Measuring the length of time to run a function

March 17, 2010
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Measuring the length of time to run a function

This post describes how to time the run time of a R function.

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Omegahat Statistical Computing » R 2010-03-16 19:28:40

March 16, 2010
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Omegahat Statistical Computing » R 2010-03-16 19:28:40

Hin-Tak Leung mailed me about a problem with certain malformed XML documents from FlowJo. There are namespace prefixes (prfx:nodeName) with no corresponding namespace declarations (xmlns:prefix=”uri”). How do we fix these? Well, the XML parser can read this but raises errors. We can do nice things to catch these errors and then post-process them. Then we

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Interrupting R processes in Ubuntu

March 16, 2010
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It's funny how things happen. Yesterday I was working away on a project in R and the unenjoyable happens---the process hangs for longer than desired. I operate R in the standard GNOME terminal in Ubuntu and the only way I knew was to close the entire a...

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