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

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 "ngCMatrix"
#>   [[ suppressing 100 column names ‘AAACGAAAGAGCGAAA-1’, ‘AAACGAAAGAGTTTGA-1’, ‘AAACGAAAGCGAGCTA-1’ ... ]]
#>                                                                               
#> OR4F5      . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> AL627309.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F29     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>                                                                               
#> OR4F5      . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> AL627309.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F29     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>                                                                           
#> OR4F5      . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> AL627309.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> OR4F29     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .