Reference

Bootstrapping Ranges Block bootstrap ranges optionally within genome segmentation
bootRanges()	Block bootstrap for genomic ranges
BootRanges-class BootRanges	BootRanges object
Segmenting genome by density
segmentDensity()	Genome segmentation based on feature density
reduceSegment()	Combine nearby regions with same state
oneRegionSegment()	Segmentation based on one region
Assessing bootstrap quality
plotSegment()	Plot genome segmentation
Matching Ranges Use a propensity score-based method to match ranges by one or more covariates.
matchRanges()	Generate a covariate-matched control set of ranges
Matched classes
Matched-class Matched	Matched objects
MatchedDataFrame-class MatchedDataFrame	MatchedDataFrame objects
MatchedGRanges-class MatchedGRanges	MatchedGRanges objects
MatchedGInteractions-class MatchedGInteractions	MatchedGInteractions objects
Assessing matching quality
overview()	Overview of matching quality
plotCovariate()	Covariate plotting for Matched objects
plotPropensity()	Propensity score plotting for Matched objects
Accessor functions
matchedData()	Get matched data from a Matched object
covariates()	Get covariates from a Matched object
method()	Get matching method used for Matched object
withReplacement()	Get replace method
indices()	Get indices of matched set
focal()	Get focal set from a Matched object
pool()	Get pool set from a Matched object
matched()	Get matched set from a Matched object
unmatched()	Get unmatched set from a Matched object
Utility functions
combnCov()	Function for creating combinations of covariates
makeExampleMatchedDataSet()	Function for generating an example matchRanges or Matched dataset