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.
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:
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
- 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.