Blog Archives

Annotated Manhattan plots and QQ plots for GWAS using R, Revisited

April 25, 2011
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Last year I showed you how to create manhattan plots, and later how to highlight regions of interest, using ggplot2 in R. The code was slow, required a lot of memory, and was difficult to maintain and modify. I finally found time to rewrite the code u...

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Using LaTeX for Math Formulas on the Web

April 20, 2011
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I love the idea of using R+LaTeX+Sweave for reproducible research. This is even easier now that R has a jazzy new IDE that supports Sweave syntax highlighting and automatic PDF generation. I know I'm going to take some flak for saying this, but let's ...

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Using R + Bioconductor to Get Flanking Sequence Given Genomic Coordinates

April 12, 2011
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I'm working on a project using next-gen sequencing to fine-map a genetic association in a gene region. Now that I've sequenced the region in a small sample, I'm picking SNPs to genotype in a larger sample. When designing the genotyping assay the lab wi...

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Monday Links: 23andMe, RStudio, PacBio+Galaxy, Data Science One-Liners, Post-Linkage RFA, SSH

April 11, 2011
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Monday Links: 23andMe, RStudio, PacBio+Galaxy, Data Science One-Liners, Post-Linkage RFA, SSH

Lately I haven't written as many full length posts as usual, but here's a quick roundup of a few links I've shared on Twitter (@genetics_blog) over the last week:First, 23andMe is having a big DNA Day Sale ($108) for the kit + 1 year of their personal ...

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Prune GWAS data in R

March 29, 2011
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Prune GWAS data in R

Hansong Wang, our biostats professor here at the Hawaii Cancer Center, generously gave me some R code that goes through a SNP annotation file (i.e. a mapfile) and selects SNPs that are at least a certain specified distance apart. You might want to do t...

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RStudio Keyboard Shortcut Reference PDF

March 21, 2011
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I recently started using RStudio, the amazing new IDE for R. You can view all of RStudio's keyboard shortcuts by going to the help menu, but I made this printable reference for myself and thought I'd share it. I only included the Windows shortcuts, and...

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New GenABEL Website, and more *ABEL software

March 18, 2011
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The *ABEL suite of R packages and software for genetic analysis has grown substantially since the appearance of GenABEL and the previously mentioned ProbABEL R packages. There are now a handful of useful R packages and other software utilities facilita...

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Forest plots using R and ggplot2

March 9, 2011
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Abhijit over at Stat Bandit posted some nice code for making forest plots using ggplot2 in R. You see these lots of times in meta-analyses, or as seen in the BioVU demonstration paper. The idea is simple - on the x-axis you have the odds ratio (or what...

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Splitting a Dataset Revisited: Keeping Covariates Balanced Between Splits

March 8, 2011
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In my previous post I showed you how to randomly split up a dataset into training and testing datasets. (Thanks to all those who emailed me or left comments letting me know that this could be done using other means. As things go with R, it's sometimes ...

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RStudio: New free IDE for R

February 28, 2011
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Just saw the announcement of the availability of Rstudio, a new (free & open source) integrated development environment for R that works on Windows, Mac, and Linux. Judging from the screenshots, it looks like Rstudio supports syntax highlighting for Sweave & easy PDF creation from Sweave code, which is something I haven't seen anywhere else (on Windows at least)....

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