anndata_filter not setting threshold
Hi,
I am trying to set a custom filter for the test data via refining_cuts
. My go_cut
looks like this:
I specifically set pct_dropout_by_counts to filter between 90-100. However, when I apply the filtering, the genes are not filtered out as seen here:
The object still contains contains values below 90. I noticed that it is because this quality measure is not implemented yet:
It would be better to make the code more general, and applying the filter regardless of what the column is called, instead of listing every single column individually. Then we don't have any issues if we add another quality measure later on. So I would propose filtering the adata.var directly and not using sc.pp.filter_genes
.