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boxiangliu / locuscomparer

LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
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implementation with zscores? #9

Open ccrobertson opened 5 years ago

ccrobertson commented 5 years ago

Hi there,

Thanks for this great tool. It is very convenient to use and makes great plots. I'm wondering if you've considered adding an option to plot zscores instead of pvalues. As you probably know, when samples sizes get large enough, pvalues are sufficiently close to zero that R and other programs cannot distinguish between them and they get truncated to some arbitrarily small number.

One could argue that we shouldn't bother trying to interpret differences between such small numbers. But i think for plotting purposes, the visual might be better if zscores were used instead of pvalues -- so you don't end up with a cluster of points on a flat line at the edge of "detection." If there's a reason you've chosen not to do this, I'd also be interested to know!

Thanks again for the great tool.

boxiangliu commented 5 years ago

Hello Cassie,

Thanks for reaching out! This is a great suggestion - something I have considered before but never got the chance to implement.

If this is a feature that you are interested in contributing, please let me know and I can give you some starters. Otherwise, it is on my list of todos and will be available for a future release.

Boxiang

ccrobertson commented 5 years ago

Hi Boxiang,

Great! It will be a couple of weeks before I get to it, but I'd be happy to contribute this feature. I should start by forking the repo right? Then can submit a pull request?

Cassie