# Binding site defintion based on iCLIP data

## Documentation for package ‘BindingSiteFinder’ version 2.9.0

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

## Help Pages

+-method | Add two 'BSFDataSet' objects
add-BSFDataSet | Add two 'BSFDataSet' objects
annotateWithScore | Annotation function for BSFDataSet object
assignToGenes | Assign binding sites to their hosting genes
assignToTranscriptRegions | Assign binding sites to their hosting transcript regions
bindingSiteCoveragePlot | Plot signal coverage of selected ranges
bindingSiteDefinednessPlot | Binding site definedness plot
BSFDataSet | BSFDataSet object and constructors
BSFDataSet, | BSFDataSet object and constructors
BSFDataSet-class, | BSFDataSet object and constructors
BSFDataSetFromBigWig | BSFDataSet object and constructors
BSFind | RBP binding site definition for iCLIP data
calculateBsBackground | Compute background coverage for binding sites per gene
calculateBsFoldChange | Compute fold-changes per binding site
calculateSignalToFlankScore | Calculate signal-to-flank score
clipCoverage | Coverage function for BSFDataSet objects
collapseReplicates | Collapse signal from replicates
combineBSF | Combine multiple 'BSFDataSet' objects
coverageOverRanges | Coverage function for BSFDataSet objects
duplicatedSitesPlot | Plot the number of overlaps when assigning crosslink sites to genes
estimateBsWidth | Function to estimate the appropriate binding site width together with the optimal gene-wise filter level.
estimateBsWidthPlot | Plot the signal-to-flank score for varying gene-wise filter and binding site width
exportTargetGenes | Function to export sorted RBP target genes
exportToBED | Wrapper function to export binding sites as BED files
filterBsBackground | Filter for genes not suitable for differential testing
geneOverlapsPlot | UpSet-plot to that shows the gene type overlaps
geneRegulationPlot | Gene Regulation Plot
getMeta | Accessor method for the meta data of the BSFDataSet object
getMeta-method | Accessor method for the meta data of the BSFDataSet object
getName | Accessor method for the name of the BSFDataSet object
getName-method | Accessor method for the name 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
globalScorePlot | Plot the PureCLIP score distribution after re-assignment
imputeBsDifferencesForTestdata | Impute artificial differences in the example data set
makeBindingSites | Define equally sized binding sites from peak calling results and iCLIP crosslink events.
makeBsSummaryPlot | Plot binding site filter diagnostics
mergeCrosslinkDiagnosticsPlot | Plot binding site merging diagnostics
mergeSummaryPlot | Plot summarized results of the different binding site merging and filtering steps
plotBsBackgroundFilter | Diagnostic plots for the differential binding background
plotBsMA | MA style plot
plotBsVolcano | Volcano style plot
processingStepsFlowChart | Step-wise flowchart plot
processingStepsTable | Create a table of all workflow steps for reporting
pureClipGeneWiseFilter | Filter PureCLIP sites by their score distribution per gene
pureClipGlobalFilter | Filter PureCLIP sites by their score distribution
pureClipGlobalFilterPlot | Plot the PureCLIP score distribution with global cutoff indicator
quickFigure | Quick figures
rangeCoveragePlot | Plot crosslink event coverage over binding site range
reproducibilityCutoffPlot | Plot to that shows how many replicates support each binding site
reproducibilityFilter | Replicate reproducibility filter function
reproducibilityFilterPlot | Plot to that shows the crosslink site distribution per replicate
reproducibilitySamplesPlot | UpSet-plot to that shows how each replicate supports binding sites
reproducibilityScatterPlot | Plot that shows binding site reproducibility as scatter
setMeta | Setter method for the meta data of the BSFDataSet object
setMeta-method | Setter method for the meta data of the BSFDataSet object
setName | Setter method for the names of the BSFDataSet object The name slot holds the name information of the dataset
setName-method | Setter method for the names of the BSFDataSet object The name slot holds the name information of the dataset
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
summary | Summary method to for the BSFDataSet
summary-method | Summary method to for the BSFDataSet
supportRatio | Support ratio function for BSFDataSet objects
supportRatioPlot | Plot that shows the binding site support ratio
targetGeneSpectrumPlot | Bar-chart to show the hosting gene types of binding sites
transcriptRegionOverlapsPlot | UpSet-plot to that shows the transcript region overlaps
transcriptRegionSpectrumPlot | Bar-chart to show the hosting transcript regions of binding sites
[-method | Subset a BSFDataSet object