8.17 Plotting GWAS results

The qq() and manhattan() functions in the qqman package let us easily create QQ and Manhattan plots to visualize our GWAS results.

# qq plot using the P (pvalues) column
qq(results$P)

# manhattan plot
manhattan(results)

SNPs with low p-values occur in peaks of multiple variants. These are not independent associations, but rather groups of variants in LD.

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