| 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 The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| condition-method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| condition<- |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| condition<--method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| 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 |
| fds-methods |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| featureExclusionMask |
Getter/Setter functions |
| featureExclusionMask, |
Getter/Setter functions |
| featureExclusionMask<- |
Getter/Setter functions |
| filterExpression-method |
Filtering FraserDataSets |
| filterExpressionAndVariability |
Filtering FraserDataSets |
| filtering |
Filtering FraserDataSets |
| filterVariability |
Filtering FraserDataSets |
| fit |
Fitting the denoising autoencoder |
| fit.FraserDataSet |
Fitting the denoising autoencoder |
| FRASER |
FRASER: Find RAre Splicing Events in RNA-seq data |
| FRASER.mcols.get |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| FRASER.rowRanges.get |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| FraserDataSet |
The FRASER dataset object |
| FraserDataSet-class |
FraserDataSet |
| N |
Getter/setter for count data |
| name |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| name-method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| name<- |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| name<--method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| nonSplicedReads |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| nonSplicedReads-method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| nonSplicedReads<- |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| nonSplicedReads<--method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| padjVals |
Getter/Setter functions |
| padjVals, |
Getter/Setter functions |
| pairedEnd |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| pairedEnd-method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| pairedEnd<- |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| pairedEnd<--method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| plotAberrantPerSample |
Visualization functions for FRASER |
| plotAberrantPerSample-method |
Visualization functions for FRASER |
| plotCountCorHeatmap |
Visualization functions for FRASER |
| plotCountCorHeatmap-method |
Visualization functions for FRASER |
| plotEncDimSearch |
Visualization functions for FRASER |
| plotEncDimSearch-method |
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 |
| plotQQ-method |
Visualization functions for FRASER |
| plotVolcano |
Visualization functions for FRASER |
| plotVolcano-method |
Visualization functions for FRASER |
| predictedMeans |
Getter/Setter functions |
| pseudocount |
Getter/Setter functions |
| psiTypes |
Available psi types |
| pVals |
Getter/Setter functions |
| pVals, |
Getter/Setter functions |
| samples |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| samples-method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| samples<- |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| samples<--method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| saveFraserDataSet |
Loading/Saving FraserDataSets |
| scanBamParam |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| scanBamParam-method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| scanBamParam<- |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| scanBamParam<--method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| strandSpecific |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| strandSpecific-method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| strandSpecific<- |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| strandSpecific<--method |
Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. " |
| subset.FRASER |
Subsetting by indices for junctions |