Identify Cells Used In Differential Testing

[armonazizi]

Hello Jeff and Ryan,

Thanks for this great tool! I'm using getMarkerFeatures to perform differential testing of peak accessibility between 2 cell clusters. Is there a way to identify or have the function return the cells that were used in doing the differential test? In other words, is there a straightforward way to obtain the cells that were returned from the internal matchBiasCellGroups function?

I'd like to obtain the bias-matched cell group IDs so that I can perform some downstream analysis and plotting that will match the output from getMarkerFeatures.

Thank you!!

-Armon

[rcorces]

I believe this info is stored in the SummarizedExperiment object under metadata(se)$MatchInfo

ArchR/R/MarkerFeatures.R

Line 297 in 968e442

metadata(pse)$MatchInfo <- matchObj

[armonazizi]

Thanks for the quick reply!