DE analysis and filter_rank_genes_groups

Hi there,

I am doing a DE analysis using the functions rank_genes_groups and filter_rank_genes_groups.
I noticed that when two groups are compared (I did not check when multiple groups are compared) the parameter min_in_group_fraction of the function filter_rank_genes_groups is used only to filter the first group.

I applied twice the functions rank_genes_groups and filter_rank_genes_groups to filter the calculated genes (I am asking that a gene is expressed in at least X% of cells).
There are mainly two possibilities, namely:

• a gene is expressed in at least X% of cells of both groups;
• a gene is expressed in at least X% of cells of either group1 or group2.

In Seurat, the function FindAllMarkers has the parameter min.pct that is used to only test the genes that are detected in a minimum fraction of min.pct cells in either group1 or group2.

It would be interesting to include these filtering steps in the filter_rank_genes_groups (maybe both strategies, i.e., both groups and either group1 or group2). What do you think?

Thanks!
Andrea

Start by reading the implementations and documentation for rank_genes_groups and filter_rank_genes_groups, focusing on how min_in_group_fraction is applied when comparing two groups. Define whether filtering should support genes detected in both groups, either group, or both strategies, then document the expected behavior and verify it against the issue's two-group example.