Create gene activity matrix — GeneActivity • Signac

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,
  fragtk = TRUE,
  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.
fragtk: Use fragtk for fast and memory-efficient data quantification. Can be TRUE/FALSE or a character vector. If TRUE, fragtk will be used and attempt to find the fragtk executable in the path. If FALSE, use the R implementation to produce the data matrix. If a character vector is provided, this should be the path to the fragtk executable and fragtk will be used. Note that fragtk uses the Paired Insertion Counting method, whereas the R implementation counts insertions. See https://crates.io/crates/fragtk for fragtk documentation.
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
)
#> Computing hash
Fragments(atac_small) <- fragments
GeneActivity(atac_small, fragtk = FALSE)
#> Extracting gene coordinates
#> Extracting reads overlapping genomic regions
#> 5 x 100 sparse Matrix of class "ngCMatrix"
#>   [[ suppressing 100 column names ‘AAACGAAAGAGAGGTA-1’, ‘AAACGAAAGCAGGAGG-1’, ‘AAACGAAAGGAAGAAC-1’ ... ]]
#>                                                                               
#> OR4F5  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> SAMD11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> NOC2L  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>                                                                               
#> OR4F5  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> SAMD11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> NOC2L  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>                                                               
#> OR4F5  . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F29 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F16 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> SAMD11 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> NOC2L  . . . . . . . . . . . . . . . . . . . . . . . . . . . .