Binding site defintion based on iCLIP data

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Documentation for package ‘BindingSiteFinder’ version 2.2.0

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

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
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