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,
  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.
verbose	Display messages
...	Additional options passed to FeatureMatrix

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)
#> Extracting gene coordinates
#> Extracting reads overlapping genomic regions
#> 3 x 100 sparse Matrix of class "dgCMatrix"
#>    [[ suppressing 100 column names ‘AAACGAAAGAGCGAAA-1’, ‘AAACGAAAGAGTTTGA-1’, ‘AAACGAAAGCGAGCTA-1’ ... ]]
#>                                                                               
#> OR4F5      . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> AL627309.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F29     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>                                                                               
#> OR4F5      . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> AL627309.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F29     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>                                                                           
#> OR4F5      . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> AL627309.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F29     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .