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Make poscounts accessible from .deseq2() #340

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BorisMuzellec opened this issue Nov 21, 2024 · 0 comments
Open

Make poscounts accessible from .deseq2() #340

BorisMuzellec opened this issue Nov 21, 2024 · 0 comments
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enhancement New feature or request good first issue Good for newcomers

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@BorisMuzellec
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Is your feature request related to a problem? Please describe.

DeseqDataSet.fit_size_factors() has a fit_type=poscounts option to take the average on positives reads only, but it is neither accessible when initializing a DeseqDataSet or when running .deseq2().

This means it can only be used by calling dds.fit_size_factors(fit_type=poscounts) manually.

Describe the solution you'd like

Add a size_factor_fit_type argument to either DeseqDataSet (in which case it would also become an attribute) or .deseq2()

Additional context
I'm wondering whether poscounts would be a better fall-back option than iterative, given how buggy the iterative mode is (cf #198).

This would introduce another difference compared with DESeq2 though.

@BorisMuzellec BorisMuzellec added enhancement New feature or request good first issue Good for newcomers labels Nov 21, 2024
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Labels
enhancement New feature or request good first issue Good for newcomers
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