How to get the common peak between all cell types? #2061
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Rivers-Lee
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At present, my idea is to first annotate the cell type, then use ArchR to carry out the overall peak calling with macs2, add PeakMatrix, and use getPeakSet function to get All peak.
Cell type-specific peaks were obtained using the getMarkerFeatures function.
Finally, The peaks specific for each cell type were deleted from All peaks, and the remaining peaks were considered to be Common to all cell types.
I would like to ask whether this idea is feasible and whether there are any potential problems. I find that currently ArchR does not provide functions to directly obtain common peak or gene.
In addition, I would like to ask whether the peak set provided by addBgdPeaks function can be equivalent to common peak?
Any answer would be greatly appreciated.
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