Question: R: Manhattan Plot of LRT Values Instead Of -Log10(p)

Question

[valentinatsar]

Hi all!

Do you know how to make a manhattan plot of LRT values instead of -log10(p) for regional heritability mapping analysis?

The results file consists of the following columns:

CHR SNP BP LRT

Many thanks!

[jared.andrews07]

I'm guessing the answers here are highly relevant to your case.

Answer 1

[bernatgel]

Hi, you might want to take a look at kpPlotManhattan from karyoploteR. With it you can create a manhattan plot with correct x coordinates and can plot any values you want. By default it will transform the values with -log10 but you can disable with with "logp=FALSE".

If you need it, you can also create zoomed plots of smaller regions (peaks, for example) and add other data such as genes or virtually anything else.