Binding site defintion based on iCLIP data

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Documentation for package ‘BindingSiteFinder’ version 1.6.0

• 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