CreateGeneActivityMatrix: Convert a peak matrix to a gene activity matrix

Description Usage Arguments

View source: R/preprocessing.R

Description

This function will take in a peak matrix and an annotation file (gtf) and collapse the peak matrix to a gene activity matrix. It makes the simplifying assumption that all counts in the gene body plus X kb up and or downstream should be attributed to that gene.

Usage

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

Arguments

peak.matrix

Matrix of peak counts

annotation.file

Path to GTF annotation file

seq.levels

Which seqlevels to keep (corresponds to chromosomes usually)

include.body

Include the gene body?

upstream

Number of bases upstream to consider

downstream

Number of bases downstream to consider

keep.sparse

Leave the matrix as a sparse matrix. Setting this option to TRUE will take much longer but will use less memory. This can be useful if you have a very large matrix that cannot fit into memory when converted to a dense form.

verbose

Print progress/messages


Seurat documentation built on Jan. 13, 2021, 7:11 p.m.