getQuickTssEnrichment-methods — getQuickTssEnrichment,DsATAC-method • ChrAccR

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

# S4 method for 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

Value

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

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

Author

Fabian Mueller