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qqman: An R package for creating Q-Q and manhattan plots from GWAS results.

Citation

If you’d like to cite qqman (appreciated but not required), please cite the publication below:

Turner, (2018). qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. Journal of Open Source Software, 3(25), 731, https://doi.org/10.21105/joss.00731

More details are found in the preprint:

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:

browseVignettes("qqman")

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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