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FoxoTech / methylprep

Python-based preprocessing software for Illumina methylation arrays
MIT License
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poobah pkl file is not generated #59

Closed moranr7 closed 3 years ago

moranr7 commented 4 years ago

Using methylprep version '1.2.11' and command : python -m methylprep -v process --all

I cannot pass the parameter --export_poobah to the function.

Any idea what is happening here ?

Thanks, Ray

marcmaxson commented 4 years ago

Looking into it. I noticed this too last week, and I assumed (in fact I know) that those p-values are all saved in each file's processed.csv in a new column.

But I could have it export those to its own pickle if that works better for you. The methylcheck.load() function will respect the p-value column in those CSVs and exclude failing probes if you ask it to.

But I imagine people would want to do this some other way and would need a p_values.pkl dataframe in other situations.

marcmaxson commented 3 years ago

I think this is resolved in v1.4.0 now.