Differential Accessibility between groups in same sample?

[jtls0n]

What would be the proper options for callOpenTiles using an ArchR project to enable downstream differential accessibility between groups of cells in the same sample?

I have biological replicates of a mixed population and I'm trying to compare between two groups of cells that are in the same sample (sample here is the 10x scATAC well and I have one sample for each of two biological replicates).

I've run into a few problems:

1. the default of cellPopulations = "ALL" in callOpenTiles seems to fail on an ArchR project if the string "ALL" doesn't exist in the cellPopLabel column.

2. With the current options I'm using, the metadata generated during callOpenTiles seems to prune information per cell that has more than one classifier per sample.

This seems to arise after the function sampleDataFromCellColData during the generation of BoolDT.

As a result, I can't run getSampleTileMatrix for those groups because they have been removed from the metadata.

Thank you!

EDIT: I was able to get closer using the development version, but maybe it will still fail in the end as the differential accessibility function expects more than two replicates.