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.
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)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- 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.