Find RAre Splicing Events in RNA-Seq Data

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Documentation for package ‘FRASER’ version 1.0.0

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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 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
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

-- 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
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

-- D --

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

-- F --

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

-- 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 --

mapSeqlevels Getter/Setter methods for the FraserDataSet
mergeCounts Count RNA-seq data

-- N --

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

-- O --

optimHyperParams Find optimal encoding dimension

-- P --

padjVals Getter/Setter functions
padjVals, Getter/Setter functions
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

-- R --

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

-- S --

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

-- V --

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

-- W --

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

-- Z --

zScore, Getter/Setter functions
zScores Getter/Setter functions

-- misc --

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