Signac: TSSEnrichment – R documentation

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TSSEnrichment

Compute TSS enrichment score per cell

Description

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

Usage

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

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

Details

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

Value

Returns a Seurat object

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)

Signac

Analysis of Single-Cell Chromatin Data

v1.2.1

MIT + file LICENSE

Authors

Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>), Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>), Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>), Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)

Initial release

2021-05-11