GeneActivity: Create gene activity matrix

In timoast/signac: Analysis of Single-Cell Chromatin Data

Create gene activity matrix

Description

Compute counts per cell in gene body and promoter region.

Usage

GeneActivity(
  object,
  assay = NULL,
  features = NULL,
  extend.upstream = 2000,
  extend.downstream = 0,
  biotypes = "protein_coding",
  max.width = 5e+05,
  process_n = 2000,
  gene.id = FALSE,
  verbose = TRUE
)

Arguments

object	A Seurat object
assay	Name of assay to use. If NULL, use the default assay
features	Genes to include. If NULL, use all protein-coding genes in the annotations stored in the object
extend.upstream	Number of bases to extend upstream of the TSS
extend.downstream	Number of bases to extend downstream of the TTS
biotypes	Gene biotypes to include. If NULL, use all biotypes in the gene annotation.
max.width	Maximum allowed gene width for a gene to be quantified. Setting this parameter can avoid quantifying extremely long transcripts that can add a relatively long amount of time. If NULL, do not filter genes based on width.
process_n	Number of regions to load into memory at a time, per thread. Processing more regions at once can be faster but uses more memory.
gene.id	Record gene IDs in output matrix rather than gene name.
verbose	Display messages

Value

Returns a sparse matrix

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
fragments <- CreateFragmentObject(
  path = fpath,
  cells = colnames(atac_small),
  validate.fragments = FALSE
)
Fragments(atac_small) <- fragments
GeneActivity(atac_small)

timoast/signac documentation built on Aug. 23, 2024, 1:48 a.m.