How to get a a peak count matrix with ArchR?

xindong95 / SCRIP

SCRIP(Single Cell Regulatory network Inference using ChIP-seq) is a tool for evaluating the binding enrichment of specific TR at single-cell resolution based on scATAC-seq.

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How to get a a peak count matrix with ArchR? #1

Closed pengshiyin closed 1 year ago

pengshiyin commented 1 year ago

Hi, I got the peak matrix with getMatrixFromProject() in ArchR, but I looked up the code and it seems that this peak matrix is not normalized. Can this peak count matrix be used in SCRIP enrich function?

xindong95 commented 1 year ago

It is possible to do so. The peak count matrix is usually binary, so it does not need much normalization. Besides, SCRIP preprocesses the peak count matrix with its default settings, and it works fine as long as the features' coordinates are correct. You can try it, and if you encounter any issues, please let me know.