get.mser: Calculate minimal saturated enrichment fold ratio

Description

Determine if the dataset has reached absolute saturation, or otherwise find minimal fold enrichment ratio above which the detection of peaks has stabilized enough to meet the saturation criteria.

Usage

get.mser(signal.data, 
  control.data, 
  n.chains = 5, 
  step.size = 1e+05, 
  chains = NULL, 
  cluster = NULL, 
  test.agreement = 0.99, 
  return.chains = F, 
  enrichment.background.scales = c(1), 
  n.steps = 1, ...)

Arguments

signal.data

signal tag vector list

control.data

control tag vector list

n.chains

number of dataset subsamples to use

step.size

subsampling step describing the saturation criteria. The criteria requires the set of detected binding sites to be stable (as described by the test.agreement param) when the number of tags in the dataset is reduced by step.size. The value can either be an integer above one, in which case it specifies a fixed number of tags, or a real value below one, in which case it specifies the fraction of tags that should be removed (e.g. 0.1 will remove 10

test.agreement

Fraction of the detected peaks that should agree between the full and subsampled datasets.

chains

optional parameter, giving pre-calculated chains

cluster

optional snow cluster to parallelize processing

return.chains

whether subsampled dataset results should be returned as well

enrichment.background.scales

one or multiple window scales at which the background tag density should be assessed. See enrichment.background.scales in find.binding.positions. If multiple scales are provided, multiple MSER estimates will be returned.

…

additional parameters should be the same as those passed to the find.binding.positions

n.steps

Value

A single, or multple (if multiple enrichment.background.scales were provided) MSER value. A value of 1 or very close to it implies that the dataset has reached absolute saturation based on the given criteria.