peak filtering

[AnjaliC4]

Before running getMarkerFeatures() with wilcox, how can I filter peaks present in more than x% of cells in a cluster? I know this can be done by exporting peak matrix and doing analysis after - but is there a way to do this in ArchR?

In addition, is it possible to specify peak as "distal" or "promoter" in getMarkerFeatures() ?

Thank you!

[rcorces]

Before running getMarkerFeatures() with wilcox, how can I filter peaks present in more than x% of cells in a cluster? I know this can be done by exporting peak matrix and doing analysis after - but is there a way to do this in ArchR?

We dont provide any mechanism to do this. The tricky part is deciding what counts as a peak. MACS2 peak calls are notoriously heterogenous so my recommendation would be to create a cutoff of normalized peak signal that you believe is correct in your dataset. ArchR doesnt provide this infrastructure so you'll have to do it yourself from the peak matrix

is it possible to specify peak as "distal" or "promoter" in getMarkerFeatures() ?

No but you can subset your peak set and recalculate the peak matrix based on the annotations provided in the peak set as desired.