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

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!

manhattan lrt values plot
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updated by bernatgel bernatgel • written by valentinatsar • valentinatsar

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

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written by jared.andrews07 jared.andrews07

1 answer

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.

manhattan plot made with the karyoploteR R package detail of a small region in a manhattan plot with genes plotted

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written by bernatgel bernatgel

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