Merge peaks from a subset of cell types using iterative overlap

[Dazcam]

Hi there,

I have run the ArchR pipeline up until the peak calling stage on a dataset derived from brain tissue and I'm looking to generate a merged peak set similar to the union peak set generated for all cell types, but only for a subset of the cell types (i.e. the neuronal cell types). In effect, I'm looking to merge the cell specific neuronal peak sets (saved in thePeakCalls directory). I would normally use something like bedtools or bedops for this but would like to use the iterative overlap method described in the ArchR docs if possible.

Note that I don't want to replace the original union peak set stored in the ArchR object, just to create a new peak set in the PeakCalls directory for all peaks detected in neurones.

Is there a function / method available to do this within ArchR?

Many Thanks.

[rcorces]

Create a new column in cellColData with NA for cells you dont want included and the rest of your neuron groups defined. Then addReproduciblePeakSet() on that column. This will replace the peak set that is associated with your project but I think it should maintain the file corresponding to the old peak set in your project directory.