Q-Q and Manhattan Plots for GWAS Data

Create Q-Q and manhattan plots for GWAS data from PLINK results.

Citation

If you'd like to cite qqman (appreciated but not required), please cite the pre-print below:

Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165.

Installation

Install the stable release from CRAN:

install.packages("qqman")

Or install directly from github using devtools

library(devtools)
install_github("stephenturner/qqman")

Or install the most recent development release with devtools (note, there be dragons here):

library(devtools)
install_github("stephenturner/qqman", ref="dev")

Load the package each time you use it:

library(qqman)

Usage

See the online package vignette for more examples:

vignette("manhattan")

Take a look at the built-in data:

head(gwasResults)

Basic manhattan plot using built-in data:

manhattan(gwasResults)

Basic Q-Q plot using built-in data:

qq(gwasResults$P)

Get help:

?manhattan
?qq

Notes

• This release is substantially simplified for the sake of maintainability and creating an R package. The old code that allows confidence intervals on the Q-Q plot and allows more flexible annotation and highlighting is still available at the version 0.0.0 tag.
• Special thanks to Dan Capurso and Tim Knutsen for useful contributions and bugfixes.
• Thanks to all the blog commenters for pointing out bugs and other issues.