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nsheff / LOLA

Locus Overlap Analysis: Enrichment of Genomic Ranges
http://code.databio.org/LOLA
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two-sided fisher test #20

Closed bmreilly closed 6 years ago

bmreilly commented 6 years ago

I was thinking it would be nice to have the option to choose which type of fisher's test to use for the enrichment, unless there is some reason why you would only check for positive enrichment?

For my work, it would be informative to know not only which regions are enriched but also which are depleted.

It is a simple change in the code to allow an option for the fisher test. For example, instead of hard-coding alternative="greater" you could include a variable fisher=c("greater","less", "two.sided")

Let me know what you think. Thanks.

nsheff commented 6 years ago

Thanks @bmreilly

I've implemented this just now in LOLA.