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neksa / mutagene

Python library and package for mutational analysis
https://www.ncbi.nlm.nih.gov/projects/mutagene/
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made enrichment not rely on mutually-excl counts, added OR #20

Closed carolinecunningham closed 5 years ago

carolinecunningham commented 5 years ago
neksa commented 5 years ago

I will merge the PR, but could you please add odds ratio (calculated based on contingency table) as one of the calculated, and possibly also reported results as a separate PR

carolinecunningham commented 5 years ago

I added the calculations for odds ratio in the get_stats function (line 167 of motifs/init.py), and it is part of the results output (see the identify_motifs() function). So the odds ratio currently is calculated and outputted by the program.

What do I need to change from how it is currently implemented?

Caroline

On Jul 26, 2019, at 5:29 PM, Alexander Goncearenco notifications@github.com wrote:

I will merge the PR, but could you please add odds ratio (calculated based on contingency table) as one of the calculated, and possibly also reported results as a separate PR

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