Please provide some background on the proposed additions or changes.
In the core module, we perform filtering of genes based on a minimum percent of cells genes must be detected in and a minimum mean gene expression. However, in the processed.rds files available on the portal, we do not do any filtering of the genes.
What are the changes that you are proposing?
We should update the core module to match the filtering that is performed to generate the files on the portal by making gene filtering optional and setting the default to turn gene filtering off.
Please describe the proposed solution.
To do this we should add a flag to control if gene filtering is true or false and set the default to false. Only then will the thresholds that are provided be used to perform filtering.
This will also require an update in the documentation of the parameters.
cbethell
commented
1 year ago
Please provide some background on the proposed additions or changes.
In the core module, we perform filtering of genes based on a minimum percent of cells genes must be detected in and a minimum mean gene expression. However, in the
processed.rdsfiles available on the portal, we do not do any filtering of the genes.What are the changes that you are proposing?
We should update the core module to match the filtering that is performed to generate the files on the portal by making gene filtering optional and setting the default to turn gene filtering off.
Please describe the proposed solution.
To do this we should add a flag to control if gene filtering is true or false and set the default to false. Only then will the thresholds that are provided be used to perform filtering. This will also require an update in the documentation of the parameters.
What potential "gotchas" do we know of?
Additional context or questions