| 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 |