Manhattan Plot with independent significant hits

Question

[en_keser]

Hi everyone,

I am looking for an R code to create a Manhattan plot with independent significant hits that I got from LD clumping. Would anyone happen to have a code for that?

Many thanks!

Answer 1

[LauferVA]

Consider using locuszoom for genomic regions small enough to warrant special clarification that the two associations are independent.

In particular the section Plotting LD with additional reference SNPs is relevant; you can show independence of two reference SNPs by using the red and blue coloration scheme as shown.

Because manhattan plots typically show the entire genome, any associations that are visually discernable as distinct from one another (i.e. there is space between the dots) are commonly assumed to be distinct association signals.