qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots

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 Pvalue 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.