One vs all comparisons

[jindalk]

Within a specific subset of clusters in my ArchR object, is it possible to perform one vs all comparison for each of them? For example, for 5 of my 10 clusters, can I compare each one of the 5 clusters to the rest 4, in a given feature space? I am not sure how to use getMarkerFeatures to force this specific behaviour.

[rcorces]

I think you could accomplish what you want in two ways:

1. Creating a new column in cellColData that explicitly maps your one-vs-all comparison
2. Setting your one group as useGroups and the all as bgdGroups