getQuickTssEnrichment-DsATAC-method: getQuickTssEnrichment-methods

In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

getQuickTssEnrichment-methods

Description

[Experimental] Quick, heuristic version of TSS enrichment to just get scores for each sample in the dataset. Useful, e.g. for single cells.

Usage

## S4 method for signature 'DsATAC'
getQuickTssEnrichment(
  .object,
  tssGr = NULL,
  sampleIds = getSamples(.object),
  tssW = 201L,
  distBg = 1900L
)

Arguments

.object	DsATAC object
tssGr	GRanges object containing TSS coordinates
sampleIds	sampleIds for which TSS enrichment should be computed
tssW	width to consider arount the TSS
distBg	number of bases flanking each TSS that will be added on each side

Details

Computes TSS enrichment as the ratio of total insertion sites at a window (of width tssW bp) directly at the TSS and 2 background regions symmetrically located (distBg bp) upstream and downstream of the TSS

Value

a vector of TSS enrichment values for each sample/cell in the dataset

Author(s)

Fabian Mueller

GreenleafLab/ChrAccR documentation built on March 22, 2023, 11:42 p.m.