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

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

Usage

estimateNoise(
  object,
  mask,
  mappable,
  map_frac = 0.5,
  win_size = 200,
  num_win = 1e+06,
  strand = "+",
  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

A GRanges object with the mappable regions.

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.

strand

The strand to consider.

inputAssay

The assay to use.

quantiles

The quantiles to calculate.

Value

A matrix with the quantiles for each sample.