p2g analysis on subset of peaks

[rojinsafavi]

I was wondering if it's possible to perform peak 2 gene analysis only on a subset of peaks?
Thank you!

[rcorces]

just subset your peakset and re-add it to your project etc

[rojinsafavi]

Thanks @rcorces

Could you please refer me to the ArchR functions that I should use? how should I subset my peakset, and how can I add that to an ArchR project to replace the current peakset or save it as a new obj?

[rcorces]

you can find all of the relevant functions here: https://www.archrproject.com/reference/index.html

getPeakSet() gives you a GRanges object of your peak set. Alter that however you want
addPeakSet() overwrites your current projects peak set
addPeakMatrix() to re-calculate the peak matrix