try to determine what is the best value for max_out_group_fraction in sc.tl.filter_rank_genes_groups.
In source code, it is set to 0.5 by default.
what exactly does it measure?
Here is my understanding based on the code.
For example in cluster 1 vs the rest
min_in_group_fraction is the percentage of genes that is expressed in cluster 1
max_out_group_fraction is the percentage of genes that is NOT expressed in the rest of cells?
If so, should it be set to 0.75 to match the min_in_group_fraction default?
or it is the percentage of genes that is expressed in the rest of cells?
Then the following code doesn’t look right.
gene_names = gene_names[
(fraction_in_cluster_matrix > min_in_group_fraction) &
(fraction_out_cluster_matrix < max_out_group_fraction) &
(fold_change_matrix > min_fold_change)
which one is correct?