Create Q-Q and manhattan plots for GWAS data from PLINK results.
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:
installpackages"qqman"
Or install directly from github using devtools
librarydevtoolsinstall_github"stephenturner/qqman"
Or install the most recent development release with devtools (note, there be dragons here):
librarydevtoolsinstall_github"stephenturner/qqman"ref="dev"
Load the package each time you use it:
libraryqqman
See the online package vignette for more examples:
vignette"manhattan"
Take a look at the built-in data:
headgwasResults
Basic manhattan plot using built-in data:
manhattangwasResults
Basic Q-Q plot using built-in data:
qqgwasResults$P
Get help:
?manhattan?qq
annotatePval=
option. See vignette for details.annotateTop=
option. See vignette for details.qq()
accepts graphical parameters the same way as manhattan()
xlim
ymax
argument in favor of allowing user to set ylim
in ...