Man pages for ZarnackGroup/BindingSiteFinder
Binding site defintion based on iCLIP data
| 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 |
| 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... |
| estimateBsWidth | Function to estimate the appropriate binding site width... |
| estimateBsWidthPlot | Plot the signal-to-flank score for varying gene-wise filter... |
| 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 |
| getName | Accessor method for the name of the BSFDataSet object |
| getRanges | Accessor method for the ranges of the BSFDataSet object |
| getSignal | Accessor method for the signal data of the BSFDataSet object |
| getSummary | 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... |
| makeBsSummaryPlot | Plot binding site filter diagnostics |
| mergeCrosslinkDiagnosticsPlot | Plot binding site merging diagnostics |
| mergeSummaryPlot | Plot summarized results of the different binding site merging... |
| 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... |
| quickFigure | Quick figures |
| rangeCoveragePlot | Plot crosslink event coverage over binding site range |
| reproducibilityCutoffPlot | Plot to that shows how many replicates support each binding... |
| reproducibilityFilter | Replicate reproducibility filter function |
| reproducibilityFilterPlot | Plot to that shows the crosslink site distribution per... |
| reproducibilitySamplesPlot | UpSet-plot to that shows how each replicate supports binding... |
| reproducibilityScatterPlot | Plot that shows binding site reproducibility as scatter |
| setMeta | Setter method for the meta data of the BSFDataSet object |
| setName | Setter method for the names of the BSFDataSet object The name... |
| setRanges | Setter method for the ranges of the BSFDataSet object The... |
| setSignal | Setter method for the signal data of the BSFDataSet object |
| setSummary | Setter method for the summary slot of the BSFDataSet object |
| show | Show method to for the BSFDataSet |
| subset-BSFDataSet | Subset a BSFDataSet object |
| summary | 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... |
