Find RAre Splicing Events in RNA-Seq Data

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Documentation for package ‘FRASER’ version 1.5.0

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A B C D F G H I K L M N O P R S V W Z misc

-- A --

aberrant-method 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

-- B --

bamFile 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. "
bamFile-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. "
bamFile<- 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. "
bamFile<--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. "
bestQ Getter/Setter functions

-- C --

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

-- D --

deltaPsiValue Getter/Setter functions
dontWriteHDF5 Getter/Setter functions
dontWriteHDF5<- Getter/Setter functions

-- F --

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

-- G --

getNonSplitReadCountsForAllSamples Count RNA-seq data
getSplitReadCountsForAllSamples Count RNA-seq data
getter_setter_functions Getter/Setter functions

-- H --

hyperParams Getter/Setter functions

-- I --

injectOutliers Inject artificial outliers in an existing fds

-- K --

K Getter/setter for count data

-- L --

length-method retrieve the length of the object (aka number of junctions)
loadFraserDataSet Loading/Saving FraserDataSets

-- M --

makeSimulatedFraserDataSet Create an simulated example data set for FRASER
mapSeqlevels 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. "
mergeCounts Count RNA-seq data
mergeExternalData Merge external data

-- N --

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. "

-- O --

optimHyperParams Find optimal encoding dimension

-- P --

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

-- R --

results-method Extracting results and aberrant splicing events
resultsByGenes Extracting results and aberrant splicing events
rho Getter/Setter functions
rho, Getter/Setter functions

-- S --

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

-- V --

verbose Getter/Setter functions
verbose<- Getter/Setter functions

-- W --

workingDir 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. "
workingDir-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. "
workingDir<- 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. "
workingDir<--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. "

-- Z --

zScore, Getter/Setter functions
zScores Getter/Setter functions

-- misc --

[-method Subsetting by indices for junctions
`featureExclusionMask<-` Getter/Setter functions