Q-Q and Manhattan Plots for GWAS Data

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


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qqman.gif

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.

News

qqman 0.1.4

  • Minor fix to location to referenced image for pandoc self-contained README.html generation.

qqman 0.1.3

  • Annotate SNPs below a p-value threshold with the annotatePval= option. See vignette for details.
  • Annotate the top SNP on each chromosome with the annotateTop= option. See vignette for details.

qqman 0.1.2

  • Does not assume that SNPs are evenly distributed across chromosomes when deciding where to place the tick in the center of the chromosome.
  • Changed single chromosome x-axis notation to use Mb instead of raw pos
  • qq() accepts graphical parameters the same way as manhattan()
  • Removed default xlim
  • Citation details on package load
  • Added axis label options
  • Removed ymax argument in favor of allowing user to set ylim in ...
  • Option to not take log of p-value

qqman 0.1.1

  • Fixed a bunch of typos in the vignette

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("qqman")

0.1.4 by Stephen Turner, 2 years ago


Browse source code at https://github.com/cran/qqman


Authors: Stephen Turner <[email protected]>


Documentation:   PDF Manual  


GPL-3 license


Imports calibrate

Suggests knitr


Imported by MAGNAMWAR, mrMLM, mrMLM.GUI.

Suggested by gap, polyRAD, solarius.


See at CRAN