# Binding site defintion based on iCLIP data

## Documentation for package ‘BindingSiteFinder’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

annotateWithScore | Annotation function for BSFDataSet object
bindingSiteCoveragePlot | Plot signal coverage of selected ranges
BSFDataSet | BSFDataSet object and constructors
BSFDataSet, | BSFDataSet object and constructors
BSFDataSet-class, | BSFDataSet object and constructors
BSFDataSetFromBigWig | BSFDataSet object and constructors
collapseReplicates | Collapse signal from replicates
coverageOverRanges | Coverage function for BSFDataSet objects
getMeta | Accessor method for the meta data of the BSFDataSet object
getMeta-method | Accessor method for the meta data of the BSFDataSet object
getRanges | Accessor method for the ranges of the BSFDataSet object
getRanges-method | Accessor method for the ranges of the BSFDataSet object
getSignal | Accessor method for the signal data of the BSFDataSet object
getSignal-method | Accessor method for the signal data of the BSFDataSet object
getSummary | Accessor method for the summary slot of the BSFDataSet object
getSummary-method | Accessor method for the summary slot of the BSFDataSet object
makeBindingSites | Define equally sized binding sites from peak calling results and iCLIP crosslink events.
mergeSummaryPlot | Plot summarized results of the different binding site merging and filtering steps
rangeCoveragePlot | Plot crosslink events coverage over range
reproducibilityFilter | Replicate reproducibility filter function
reproducibiliyCutoffPlot | Plot to that shows how many replicates support each binding site
setMeta | Setter method for the meta data of the BSFDataSet object
setMeta-method | Setter method for the meta data of the BSFDataSet object
setRanges | Setter method for the ranges of the BSFDataSet object The GRanges object that holds the genomic ranges information can be replaced.
setRanges-method | Setter method for the ranges of the BSFDataSet object The GRanges object that holds the genomic ranges information can be replaced.
setSignal | Setter method for the signal data of the BSFDataSet object
setSignal-method | Setter method for the signal data of the BSFDataSet object
setSummary | Setter method for the summary slot of the BSFDataSet object
setSummary-method | Setter method for the summary slot of the BSFDataSet object
show | Show method to for the BSFDataSet
show-method | Show method to for the BSFDataSet
subset-BSFDataSet | Subset a BSFDataSet object
supportRatio | Support ratio function for BSFDataSet objects
supportRatioPlot | Plot that shows the binding site support ratio
[-method | Subset a BSFDataSet object