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totajuliusd / topr

topr is a collection of plotting functions for visualizing and exploring genetic association results. Association results from multiple phenotypes can be viewed simultaneously, over the entire genome (Manhattan plot) or in the more detailed regional view.
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Plotting very small p-values #16

Closed eavalo closed 9 months ago

eavalo commented 1 year ago

Hi Tota,

Great package!

I was trying to make a locuszoom style plot of a region where the strongest association signal has pvalues ~1e-400 . Since R can only represent values around ~1e-300 this does not work.

One way to get around this would be to allow to pass the p-values as log10 transformed.

Best,

Erkka

totajuliusd commented 1 year ago

Hi Erkka and thank you for pointing this out and coming up with the solution to this problem. This will be fixed in the next version of topr which will be released soon. Thanks, Tota

dhamelse commented 9 months ago

Hi, where can I find the functionality to input significance as log10p? running into the same issue, but hopeful it has been resolved!

totajuliusd commented 9 months ago

Hi, it has not been resolved in the current version but will be in the next one, which will be released within the next few days.

totajuliusd commented 9 months ago

Hi again, topr v.2.0.0 is now available (here and on CRAN), and this version can take input data as log10 p-values, if you provide the functions with the following argument (log_trans_p=F)