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Is your feature request related to a problem? Please describe.
DeseqDataSet.fit_size_factors() has a fit_type=poscountsoption 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.
The text was updated successfully, but these errors were encountered:
Is your feature request related to a problem? Please describe.
DeseqDataSet.fit_size_factors()
has afit_type=poscounts
option to take the average on positives reads only, but it is neither accessible when initializing aDeseqDataSet
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 eitherDeseqDataSet
(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 thaniterative
, given how buggy theiterative
mode is (cf #198).This would introduce another difference compared with DESeq2 though.
The text was updated successfully, but these errors were encountered: