getMarkerFeatures() all groups vs specific group

[rcorces]

Discussed in https://github.com/GreenleafLab/ArchR/discussions/1448

^{Originally posted by **wuv21** June 2, 2022} Hi! Just a conceptual question regarding getMarkerFeatures() (and to make sure I'm understanding this function correctly): I understand that getMarkerFeatures() as used below will return a list of markers that are unique to each group in the `groupBy` column data. If I understand correctly, the background group is set to all other cells not in the current group being examined. ```r getMarkerFeatures(proj, groupBy = "myGroup") ``` However, if I run the below code instead - should I expect the same list of significant markers as compared to markers that are specific to Group_Level_1 from the above code? When I try it out on my data, I don't see the same list of significant markers. Any clarification on this would be greatly appreciated! ```r getMarkerFeatures(proj, groupBy = "myGroup", useGroups = "Group_Level_1") ``` Thanks!

[rcorces]

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[wuv21]

1409 by @anastasiya-pendragon might contain an elegant fix for this.

[rcorces]

@wuv21 The changes suggested by @anastasiya-pendragon have now been implemented in the dev branch which will eventually be incorporated into a stable release_1.0.3. See https://github.com/GreenleafLab/ArchR/commit/23ef3cf1ab039b30aa9daf3112416c79fd32e9ac for incorporation