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nsheff / LOLA

Locus Overlap Analysis: Enrichment of Genomic Ranges
http://code.databio.org/LOLA
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OddsRatio or logOddsRatio ? #23

Closed gouthamatla closed 6 years ago

gouthamatla commented 6 years ago

Hi,

I have a question. fisher.test returns the odds ratio ( estimate ). I could not find in the code that the odds ratio is been converted to logOddsRatio. Does the runLOLA outputs odds ratio or logOddsRatio ?

nsheff commented 6 years ago

The original version mislabeled the column logOddsRatio. It should have been labled oddsRatio.

This was corrected in commit 1347ccab6c3fef5f652e8933f240d2b11971c08f See this line: https://github.com/nsheff/LOLA/blob/0f722fb3bc2d877f2341a561d50aef70aeb47964/R/calcLocEnrichment.R#L180

The dev version on bioc is updated so it should be fixed in the next bioc release.

nsheff commented 6 years ago

This is now corrected in the released version of LOLA.