ArchR doublet detection adjustment for homotypic doublets?

[RegnerM2015]

Very cool R package and great documentation!

I wanted to clarify ArchR's doublet detection approach. I understand ArchR finds heterotypic doublets, as most methods do. However, it is not quite clear in the documentation whether addDoubletScores() adjusts for the proportion of homotypic doublets.

DoubletFinder implements an optional procedure to adjust for the proportion of homotypic doublets based on how many "cell types" exist in the data set (https://github.com/chris-mcginnis-ucsf/DoubletFinder).

My question is whether ArchR's addDoubletScores() function implements a similar procedure "under the hood"?

[jgranja24]

Hi @RegnerM2015,

Currently, ArchR does not do this, but I am interested in looking into this adjustment. This seems like a post-hoc adjustment rather would be an option to filterDoublets rather than addDoubletScores. Does that seem reasonable?

Best

Jeff

[RegnerM2015]

I agree this adjustment seems more appropriate in filterDoublets rather than addDoubletScores

Thanks for clarifying!