Calculate the divergent loci complexity of a CTSS dataset. — calcDivergentLociComplexity • PRIME

This function calculates the divergent loci complexity of a given CTSS dataset.

Usage

calcDivergentLociComplexity(
  object,
  loci,
  step = 1e+06,
  CTSSunexpressed = 1,
  lociunexpressed = 2,
  requirebidirectional = FALSE,
  minCTSSsupport = 2
)

Arguments

object: A RangedSummarizedExperiment resulting from CAGEfightR::quantifyCTSSs().
loci: A GRanges object containing the tag clusters from which divergent loci should be called.
step: The step size for the subsampling.
CTSSunexpressed: The count threshold for considering a CTSS to be unexpressed.
lociunexpressed: The count threshold for considering a tag cluster to be unexpressed.
requirebidirectional: Logical indicating whether to require bidirectional transcription for a divergent locus from the same sample.
minCTSSsupport: The minimum number of samples a CTSS must be expressed in to be considered.

Value

A data frame containing the number of divergent loci (column "numberLoci") for each sample and target (column "totalTags").