Is your feature request related to a problem? Please describe.
The DeseqDataSet and DeseqStats classes print a message at each step of the pipeline (e.g. fitting size factors, or dispersions), including when those steps are nested within another task (e.g., computing VST #99), which can lead to many useless statements being printed.
Describe the solution you'd like
Having a verbosity parameter that would allow controlling the desired level of verbosity of fit_size_factors, fit_genewise_dispersions, fit_dispersion_trend, and so on.
Describe alternatives you've considered
Deactivating print statements from nested calls (e.g. VST).
Additional context
Currently, computing VST (#99) prints the following:
Is your feature request related to a problem? Please describe.
The
DeseqDataSetandDeseqStatsclasses print a message at each step of the pipeline (e.g. fitting size factors, or dispersions), including when those steps are nested within another task (e.g., computing VST #99), which can lead to many useless statements being printed.Describe the solution you'd like
Having a verbosity parameter that would allow controlling the desired level of verbosity of
fit_size_factors,fit_genewise_dispersions,fit_dispersion_trend, and so on.Describe alternatives you've considered
Deactivating print statements from nested calls (e.g. VST).
Additional context
Currently, computing VST (#99) prints the following: