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Seurat V3 has a function CreateGeneActivityMatrix, which can convert ATAC peaks to gene-level's matrix.

Here is the prototype:

CreateGeneActivityMatrix(
  peak.matrix,
  annotation.file,
  seq.levels = c(1:22, "X", "Y"),
  include.body = TRUE,
  upstream = 2000,
  downstream = 0,
  verbose = TRUE
)

Here are my questions:

  1. I want to know what is the format of the first parameter peak.matrix ? For example, what are the row names of this matrix? (Is there a strict rule of the row names?)
  2. The parameter seq.levels. Besides 1...22,X,Y , Can I add other chromosome ? like hs37d5
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