Bootstrapping Ranges

Block bootstrap ranges optionally within genome segmentation

bootRanges()

Block bootstrap for genomic ranges

segmentDensity()

Genome segmentation based on feature density

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 objects

MatchedDataFrame-class

MatchedDataFrame objects

MatchedGRanges-class

MatchedGRanges objects

MatchedGInteractions-class

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