misc/paper/paper.md

In stephenturner/qqman: Q-Q and Manhattan Plots for GWAS Data

title: 'qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots' tags: - R - genetic epidemiology - gwas - manhattan plot authors: - name: Stephen D. Turner orcid: 0000-0001-9140-9028 affiliation: "1, 2" # (Multiple affiliations must be quoted) affiliations: - name: Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville Virginia 22908 index: 1 - name: Bioinformatics Core, University of Virginia School of Medicine, Charlottesville Virginia 22908 index: 2 date: 25 April 2018 bibliography: paper.bib

Summary

Genome-wide association studies (GWAS) have been successful in identifying thousands of trait and disease-associated single nucleotide polymorphisms (SNPs). The primary result of a GWAS analysis is a list of SNPs, their associated chromosomal position, and a P-value representing the statistical significance of the association. A commonly used method used to visualize GWAS results is the "manhattan plot" -- a plot of the $-log_{10}(P)$ of the association statistic on the y-axis versus the chromosomal position of the SNP on the x-axis. Another commonly used results diagnostic plot is the quantile-quantile ("Q-Q") plot. Q-Q plots display the observed association P-value for all SNPs on the y-axis versus the expected uniform distribution of P-values under the null hypothesis of no association on the x-axis.

One of the most commonly used software packages for manipulating and analyzing GWAS data is PLINK (@purcell2007plink). qqman is an R package that allows for quick and flexible generation of publication-ready Q-Q and manhattan plots directly from PLINK results files. The qqman package is a user-friendly tool to visualize results from GWAS experiments using Q-Q and manhattan plots. The manhattan() function in the qqman package takes a data frame with columns containing the chromosome number, chromosomal position, P-value, and optionally the SNP name. By default, manhattan() looks for column names corresponding to those output by the plink --assoc command, namely, "CHR," "BP," "P," and "SNP," although different column names can be specified by the user. Thresholds for suggestive and genome-wide significance are drawn, and users also have the ability to highlight/annotate SNPs of interest. Finally, the qq() function can be used to generate a Q-Q plot to visualize the distribution of association P-values. An example of the plots produced by qqman is shown in Figure 1.

These graphics can be created in other software, such as the standalone desktop software Haploview (@barrett2004haploview), or for focused regions using the web-based application LocusZoom (@pruim2010locuszoom). Conversely, qqman is distributed as an R package with no other dependencies that can be easily integrated into existing R-based scripted workflows to further enable automated reproducible research. Furthermore, users can take advantage of R's very granular control of graphical output, enabling a high degree of customizability in creating high-resolution, publication-ready figures. The qqman package ships with example data and a detailed vignette illustrating its usage and further features not described here. The package is available on GitHub under the GNU General Public License at https://github.com/stephenturner/qqman and on the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/package=qqman.

References

stephenturner/qqman documentation built on Aug. 25, 2023, 10:17 a.m.