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Identify divergent loci from tag clusters with summit centering. The function is similar to divergentLociSummit but does not require tag clusters to be passed to the function. This is handeled internally by calling CAGEfightR::clusterUnidirectionally on the pooled CTSS signal.

Source: R/divergent.R
divergentLociTCsSummit.Rd

Identify divergent loci from tag clusters with summit centering. The function is similar to divergentLociSummit but does not require tag clusters to be passed to the function. This is handeled internally by calling CAGEfightR::clusterUnidirectionally on the pooled CTSS signal.

Usage

divergentLociTCsSummit(
  ctss,
  max_gap = 400,
  win_size = 200,
  inputAssay = "counts",
  callingAssay = "counts"
)

Arguments

ctss

A RangedSummarizedExperiment resulting from CAGEfightR::quantifyCTSSs().

max_gap

Maximum distance between tag clusters to be considered part of a divergent locus.

win_size

Size of the flanking windows around the midpoint of the divergent locus.

inputAssay

The assay to use for quantification.

callingAssay

The assay to use for calling TCs.

Value

A GRanges object containing the divergent loci.