How to get peak by cell matrix from ChromatinAssay class of Seurat object?

[ananyapavuluri]

Hello, I am brand new to Seurat and Signac. I have a large Seurat object (S4 object of class Seurat) representing an scATAC-seq experiment. Under assays, I have ATAC which is an S4 object of class ChromatinAssay, and under this, there is counts which is of class dgCMatrix.

I am wondering how I can extract the peak by cell matrix from counts, and am also wondering what i and p represent under counts, becausei is not matching the number of peaks that should be in the matrix.

[timoast]

Hi, you can use the GetAssayData() function

The i, p slots are part of the internal data representation for a sparse matrix. Please do not interact with those slots directly