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

April 25, 2011
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(This article was first published on Getting Genetics Done, and kindly contributed to R-bloggers)

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 using base graphics rather than ggplot2. The code is now much faster, and if you're familiar with base R's plot options and graphical parameters,

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