CreateGeneActivityMatrix: Convert a peak matrix to a gene activity matrix

In gcday/seurat_fresh: Tools for Single Cell Genomics

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

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

gcday/seurat_fresh documentation built on June 23, 2019, 12:02 a.m.