+-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 |