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:
- 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?) - The parameter
seq.levels
. Besides 1...22,X,Y , Can I add other chromosome ? likehs37d5