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 set. I recently had to update this function to allow me to color code SNPs of interest, similar to the plots shown in figure 1 of Cristen Willer’s

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