TSSEnrichment function

Compute TSS enrichment score per cell

Compute the transcription start site (TSS) enrichment score for each cell, as defined by ENCODE: https://www.encodeproject.org/data-standards/terms/.

TSSEnrichment(
  object,
  tss.positions = NULL,
  n = NULL,
  fast = TRUE,
  assay = NULL,
  cells = NULL,
  process_n = 2000,
  verbose = TRUE,
  region_extension = 1000
)

Arguments

• object: A Seurat object

• tss.positions: A GRanges object containing the TSS positions. If NULL, use the genomic annotations stored in the assay.

• n: Number of TSS positions to use. This will select the first n TSSs from the set. If NULL, use all TSSs (slower).

• fast: Just compute the TSS enrichment score, without storing the base-resolution matrix of integration counts at each site. This reduces the memory required to store the object but does not allow plotting the accessibility profile at the TSS.

• assay: Name of assay to use

• cells: A vector of cells to include. If NULL (default), use all cells in the object

• process_n: Number of regions to process at a time if using fast

  option.

• verbose: Display messages

• region_extension: Distance extended upstream and downstream from TSS in which to calculate enrichment and background.

Returns

Returns a Seurat object

Details

The computed score will be added to the object metadata as "TSS.enrichment".

Examples

## Not run:

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
Fragments(atac_small) <- CreateFragmentObject(
  path = fpath,
  cells = colnames(atac_small),
  tolerance = 0.5
)
TSSEnrichment(object = atac_small)
## End(Not run)