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Additional parameters min_fract_pos and min_cells_per_group in perform_dge() #180

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llumdi opened this issue Oct 25, 2021 · 0 comments
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@llumdi
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llumdi commented Oct 25, 2021

We are repeatedly asked to filter out lowly expressed genes before performing DGE analysis.

Currently, I only have a workaround by filtering the provided DGE results, but the correct way would be to filter them before applying the DGE test. Would it be possible to add such a parameter (e.g min_fract_pos) to the functions perform_dge() and get_de() , so that a gene should be positive > min_fract_pos in at least one group.
This parameter is routinely used in seurat FindMarkers(), see: https://www.rdocumentation.org/packages/Seurat/versions/2.3.0/topics/FindMarkers

PS: I would also include a min_cells_per_group in get_de(), as it's already the case for perform_dge()

@llumdi llumdi added the enhancement New feature or request label Oct 25, 2021
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