GeneActivity function

Create gene activity matrix

Compute counts per cell in gene body and promoter region.

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

Returns

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)