A B C D F G H I K L M N O P R S V W Z misc
| aberrant | Extracting results and aberrant splicing events |
| addCountsToFraserDataSet | Count RNA-seq data |
| annotateRanges | Annotates the given FraserDataSet with the HGNC symbol with biomaRt |
| annotateRangesWithTxDb | Annotates the given FraserDataSet with the HGNC symbol with biomaRt |
| assayNames-method | Returns the assayNames of FRASER |
| assays-method | Returns the assay for the given name/index of the FraserDataSet |
| assays<--method | Returns the assay for the given name/index of the FraserDataSet |
| bamFile | Getter/Setter methods for the FraserDataSet |
| bamFile-method | Getter/Setter methods for the FraserDataSet |
| bamFile<- | Getter/Setter methods for the FraserDataSet |
| bamFile<--method | Getter/Setter methods for the FraserDataSet |
| bestQ | Getter/Setter functions |
| calculatePadjValues | FRASER: Find RAre Splicing Events in RNA-seq data |
| calculatePSIValues | PSI value calculation |
| calculatePvalues | FRASER: Find RAre Splicing Events in RNA-seq data |
| calculateZscore | FRASER: Find RAre Splicing Events in RNA-seq data |
| condition | Getter/Setter methods for the FraserDataSet |
| condition-method | Getter/Setter methods for the FraserDataSet |
| condition<- | Getter/Setter methods for the FraserDataSet |
| condition<--method | Getter/Setter methods for the FraserDataSet |
| countNonSplicedReads | Count RNA-seq data |
| countRNA | Count RNA-seq data |
| countRNAData | Count RNA-seq data |
| counts-method | Getter/setter for count data |
| counts<--method | Getter/setter for count data |
| countSplitReads | Count RNA-seq data |
| createTestFraserDataSet | Create a test dataset |
| createTestFraserSettings | Create a test dataset |
| currentType | Getter/Setter functions |
| currentType<- | Getter/Setter functions |
| deltaPsiValue | Getter/Setter functions |
| dontWriteHDF5 | Getter/Setter functions |
| dontWriteHDF5<- | Getter/Setter functions |
| featureExclusionMask | Getter/Setter functions |
| featureExclusionMask, | Getter/Setter functions |
| featureExclusionMask<- | Getter/Setter functions |
| filterExpression | Filtering FraserDataSets |
| filterExpressionAndVariability | Filtering FraserDataSets |
| filtering | Filtering FraserDataSets |
| filterVariability | Filtering FraserDataSets |
| fit | FRASER: Find RAre Splicing Events in RNA-seq data |
| FRASER | FRASER: Find RAre Splicing Events in RNA-seq data |
| FRASER.mcols.get | Getter/Setter methods for the FraserDataSet |
| FRASER.rowRanges.get | Getter/Setter methods for the FraserDataSet |
| FraserDataSet | The FRASER dataset object |
| FraserDataSet-class | FraserDataSet |
| getNonSplitReadCountsForAllSamples | Count RNA-seq data |
| getSplitReadCountsForAllSamples | Count RNA-seq data |
| getter_setter_functions | Getter/Setter functions |
| hyperParams | Getter/Setter functions |
| injectOutliers | Inject artificial outliers in an existing fds |
| K | Getter/setter for count data |
| length-method | retrieve the length of the object (aka number of junctions) |
| loadFraserDataSet | Loading/Saving FraserDataSets |
| mapSeqlevels | Getter/Setter methods for the FraserDataSet |
| mergeCounts | Count RNA-seq data |
| N | Getter/setter for count data |
| name | Getter/Setter methods for the FraserDataSet |
| name-method | Getter/Setter methods for the FraserDataSet |
| name<- | Getter/Setter methods for the FraserDataSet |
| name<--method | Getter/Setter methods for the FraserDataSet |
| nonSplicedReads | Getter/Setter methods for the FraserDataSet |
| nonSplicedReads-method | Getter/Setter methods for the FraserDataSet |
| nonSplicedReads<- | Getter/Setter methods for the FraserDataSet |
| nonSplicedReads<--method | Getter/Setter methods for the FraserDataSet |
| optimHyperParams | Find optimal encoding dimension |
| padjVals | Getter/Setter functions |
| padjVals, | Getter/Setter functions |
| pairedEnd | Getter/Setter methods for the FraserDataSet |
| pairedEnd-method | Getter/Setter methods for the FraserDataSet |
| pairedEnd<- | Getter/Setter methods for the FraserDataSet |
| pairedEnd<--method | Getter/Setter methods for the FraserDataSet |
| plotAberrantPerSample | Visualization functions for FRASER |
| plotCountCorHeatmap | Visualization functions for FRASER |
| plotEncDimSearch | Visualization functions for FRASER |
| plotExpectedVsObservedPsi | Visualization functions for FRASER |
| plotExpression | Visualization functions for FRASER |
| plotFilterExpression | Visualization functions for FRASER |
| plotFilterVariability | Visualization functions for FRASER |
| plotFunctions | Visualization functions for FRASER |
| plotQQ | Visualization functions for FRASER |
| plotVolcano | Visualization functions for FRASER |
| predictedMeans | Getter/Setter functions |
| pseudocount | Getter/Setter functions |
| psiTypes | Available psi types |
| pVals | Getter/Setter functions |
| pVals, | Getter/Setter functions |
| results | Extracting results and aberrant splicing events |
| results-method | Extracting results and aberrant splicing events |
| resultsByGenes | Extracting results and aberrant splicing events |
| rho | Getter/Setter functions |
| rho, | Getter/Setter functions |
| samples | Getter/Setter methods for the FraserDataSet |
| samples-method | Getter/Setter methods for the FraserDataSet |
| samples<- | Getter/Setter methods for the FraserDataSet |
| samples<--method | Getter/Setter methods for the FraserDataSet |
| saveFraserDataSet | Loading/Saving FraserDataSets |
| scanBamParam | Getter/Setter methods for the FraserDataSet |
| scanBamParam-method | Getter/Setter methods for the FraserDataSet |
| scanBamParam<- | Getter/Setter methods for the FraserDataSet |
| scanBamParam<--method | Getter/Setter methods for the FraserDataSet |
| strandSpecific | Getter/Setter methods for the FraserDataSet |
| strandSpecific-method | Getter/Setter methods for the FraserDataSet |
| strandSpecific<- | Getter/Setter methods for the FraserDataSet |
| strandSpecific<--method | Getter/Setter methods for the FraserDataSet |
| subset.FRASER | Subsetting by indices for junctions |
| verbose | Getter/Setter functions |
| verbose<- | Getter/Setter functions |
| workingDir | Getter/Setter methods for the FraserDataSet |
| workingDir-method | Getter/Setter methods for the FraserDataSet |
| workingDir<- | Getter/Setter methods for the FraserDataSet |
| workingDir<--method | Getter/Setter methods for the FraserDataSet |
| zScore, | Getter/Setter functions |
| zScores | Getter/Setter functions |
| [-method | Subsetting by indices for junctions |
| `featureExclusionMask<-` | Getter/Setter functions |