Major update to coloc package

I am a co-author on another paper about colocalisation posted on arXiv. It’s a novel approach, using Bayesian inference based on Approximate Bayes Factors derived from p values, making colocalisation testing much more practical when data is not often as open access as claimed. My co-author, Vincent Plagnol, has written a nice post about it on Haldane’s Sieve.

The software to conduct these tests has been included in my coloc package, and I think such a change deserves a bump in version, so coloc v2.0 is now available on CRAN, together with a new vignette, explaining the different methods of analysis available, but see the papers 1 2 for the nitty gritty.

Writing R vignettes in emacs org mode using ox-ravel

I want to be able to write R vignettes in org-mode. Crazy, perhaps, but it has become my default way to write everything, notes on current projects, even beamer slides and papers. Now I need to write a vignette for the coloc R package, and switching to Sweave reminds me what a pain that is. So I had a play with knitr before, and liked it, but again it means learning a new markup syntax.

I have found ox-ravel, which means I can now write .org files, and export part or all to Sweave, knitr, brew, etc. I cannot stress just how fantastic this is, in allowing me to write everything in one syntax!

But setting it up required updating org-mode, because it requires the new ox export engine found in org-8. In the process, I didn’t want to break org2blog which I use to write these blog posts. Knowing this could get complicated, I documented each step here.

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snpStatsWriter v1.5-1 and knitr vignettes

A new version of snpStatsWriter is up on CRAN. It includes a new function, write.snphap(), for writing snphap files, and a brief vignette has been added, my first vignette written in markdown with knitr.

I’m not absolutely sure I want to learn another markdown syntax, I spend so much time in Org mode that translating from one to another is a pain, but I wanted to give knitr a go and markdown is friendlier than Sweave-like syntax. Perhaps next time I will try ravel to combine org-mode and knitr.

Anyway, it worked well, and you can see the markdown vignette source and resulting html.