Estimate divergent loci noise in a given CTSS dataset by sampling and quantifying regions of a fixed size across the genome.

Usage

estimateDivergentNoise(
  object,
  mask,
  mappable_minus,
  mappable_plus,
  map_frac = 0.5,
  win_size = 200,
  num_win = 1e+06,
  inputAssay = "counts",
  quantiles = c(0.9, 0.95, 0.99, 0.999, 0.9999, 0.99999)
)

Arguments

object: A RangedSummarizedExperiment object.
mask: A GRanges object with the masked regions.
mappable_minus: A GRanges object with the mappable regions for the minus strand.
mappable_plus: A GRanges object with the mappable regions for the plus strand.
map_frac: The fraction of bases that need to be mappable.
win_size: The size of the windows to use.
num_win: The number of windows to sample.
inputAssay: The assay to use.
quantiles: The quantiles to calculate.

Value

A matrix with the quantiles for each sample.