Analysis of Alternative Splicing Using RNA-Seq

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Documentation for package ‘ASpli’ version 2.0.0

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A B C D E F G I J L M P R S T W

ASpli-package Analysis of Alternative Splicing Using RNAseq

-- A --

altPSI Accessors for ASpliAS object
altPSI-method Class '"ASpliAS"'
altPSI<- Accessors for ASpliAS object
altPSI<--method Class '"ASpliAS"'
anchorbased Accessors for ASpliSplicingReport object
anchorbased-method Class '"ASpliSplicingReport"'
anchorbased<- Accessors for ASpliSplicingReport object
anchorbased<--method Class '"ASpliSplicingReport"'
anchorc Accessors for ASpliJDU object
anchorc-method Class '"ASpliJDU"'
anchorc<- Accessors for ASpliJDU object
anchorc<--method Class '"ASpliJDU"'
anchorj Accessors for ASpliJDU object
anchorj-method Class '"ASpliJDU"'
anchorj<- Accessors for ASpliJDU object
anchorj<--method Class '"ASpliJDU"'
AsDiscover Report PSI, PJU and PIR using experimental junctions
AsDiscover-method Class '"ASpliCounts"'
ASpli Analysis of Alternative Splicing Using RNAseq
ASpli-deprecated Deprecated functions in package 'ASpli'
ASpliAS Class '"ASpliAS"'
ASpliAS-class Class '"ASpliAS"'
aspliASexample Example Aspli objects
aspliBamsExample Example Aspli objects
ASpliCounts Class '"ASpliCounts"'
ASpliCounts-class Class '"ASpliCounts"'
aspliCountsExample Example Aspli objects
ASpliDU Class '"ASpliDU"'
ASpliDU-class Class '"ASpliDU"'
aspliDUexample1 Example Aspli objects
aspliDUexample2 Example Aspli objects
aspliExampleBamList Example Aspli objects
aspliExampleGTF Example Aspli objects
ASpliFeatures-class Class '"ASpliFeatures"'
aspliFeaturesExample Example Aspli objects
ASpliIntegratedSignals Class '"ASpliIntegratedSignals"'
ASpliIntegratedSignals-class Class '"ASpliIntegratedSignals"'
ASpliJDU Class '"ASpliJDU"'
ASpliJDU-class Class '"ASpliJDU"'
aspliJunctionDUexample Example Aspli objects
ASpliSplicingReport Class '"ASpliSplicingReport"'
ASpliSplicingReport-class Class '"ASpliSplicingReport"'
aspliTargetsExample Example Aspli objects

-- B --

binbased Accessors for ASpliSplicingReport object
binbased-method Class '"ASpliSplicingReport"'
binbased<- Accessors for ASpliSplicingReport object
binbased<--method Class '"ASpliSplicingReport"'
binGenome Feature coordinates extraction
binGenome-method Feature coordinates extraction
binGenome-methods Feature coordinates extraction
binsDU Accessors for ASpliDU object
binsDU-method Class '"ASpliDU"'
binsDU<- Accessors for ASpliDU object
binsDU<--method Class '"ASpliDU"'

-- C --

condition.order Accessors for ASpliCounts object
condition.order-method Class '"ASpliCounts"'
containsGenesAndBins Examine ASpliDU objects
containsGenesAndBins-method Class '"ASpliDU"'
containsJunctions Examine ASpliDU objects
containsJunctions-method Class '"ASpliDU"'
countsb Accessors for ASpliCounts object
countsb-method Class '"ASpliCounts"'
countsb<- Accessors for ASpliCounts object
countsb<--method Class '"ASpliCounts"'
countse1i Accessors for ASpliCounts object
countse1i-method Class '"ASpliCounts"'
countse1i<- Accessors for ASpliCounts object
countse1i<--method Class '"ASpliCounts"'
countsg Accessors for ASpliCounts object
countsg-method Class '"ASpliCounts"'
countsg<- Accessors for ASpliCounts object
countsg<--method Class '"ASpliCounts"'
countsie2 Accessors for ASpliCounts object
countsie2-method Class '"ASpliCounts"'
countsie2<- Accessors for ASpliCounts object
countsie2<--method Class '"ASpliCounts"'
countsj Accessors for ASpliCounts object
countsj-method Class '"ASpliCounts"'
countsj<- Accessors for ASpliCounts object
countsj<--method Class '"ASpliCounts"'

-- D --

DUreport Differential gene expression and differential bin usage estimation
DUreport-method Class '"ASpliCounts"'
DUreport.norm Differential gene expression and differential bin usage estimation
DUreport.norm-method Class '"ASpliCounts"'
DUreport.offset Differential gene expression and differential bin usage estimation
DUreport.offset-method Class '"ASpliCounts"'
DUreportBinSplice Differential gene expression and differential bin usage estimation
DUreportBinSplice-method Class '"ASpliCounts"'

-- E --

esPSI Accessors for ASpliAS object
esPSI-method Class '"ASpliAS"'
esPSI<- Accessors for ASpliAS object
esPSI<--method Class '"ASpliAS"'
exportIntegratedSignals Export integrated signals.
exportIntegratedSignals-method Class '"ASpliIntegratedSignals"'
exportSplicingReports Export splicing reports
exportSplicingReports-method Class '"ASpliSplicingReport"'

-- F --

featuresb Accessors for ASpliFeatures object
featuresb-method Class '"ASpliFeatures"'
featuresb<- Accessors for ASpliFeatures object
featuresb<--method Class '"ASpliFeatures"'
featuresg Accessors for ASpliFeatures object
featuresg-method Class '"ASpliFeatures"'
featuresg<- Accessors for ASpliFeatures object
featuresg<--method Class '"ASpliFeatures"'
featuresj Accessors for ASpliFeatures object
featuresj-method Class '"ASpliFeatures"'
featuresj<- Accessors for ASpliFeatures object
featuresj<--method Class '"ASpliFeatures"'
filterDU Filtering ASpliDU objects
filterDU-method Class '"ASpliDU"'
filters Accessors for ASpliIntegratedSignals object
filters-method Class '"ASpliIntegratedSignals"'
filters<- Accessors for ASpliIntegratedSignals object
filters<--method Class '"ASpliIntegratedSignals"'
filterSignals Filter signals
filterSignals-method Class '"ASpliSplicingReport"'

-- G --

gbCounts Summarize read overlaps
gbCounts-method Class '"ASpliFeatures"'
gbDUreport Differential gene expression and differential bin usage estimation
gbDUreport-method Class '"ASpliCounts"'
genesDE Accessors for ASpliDU object
genesDE-method Class '"ASpliDU"'
genesDE<- Accessors for ASpliDU object
genesDE<--method Class '"ASpliDU"'
getConditions Retrieve condition names from a targets data frame.

-- I --

integrateSignals Integrate signals
integrateSignals-method Class '"ASpliSplicingReport"'
irPIR Accessors for ASpliAS object
irPIR-method Class '"ASpliAS"'
irPIR<- Accessors for ASpliAS object
irPIR<--method Class '"ASpliAS"'

-- J --

jalt Accessors for ASpliJDU object
jalt-method Class '"ASpliJDU"'
jalt<- Accessors for ASpliJDU object
jalt<--method Class '"ASpliJDU"'
jCounts Report PSI, PJU and PIR using experimental junctions
jCounts-method Class '"ASpliCounts"'
jDUreport Differential junction usage estimation
jDUreport-method Class '"ASpliAS"'
jDUreport-method Class '"ASpliJDU"'
jes Accessors for ASpliJDU object
jes-method Class '"ASpliJDU"'
jes<- Accessors for ASpliJDU object
jes<--method Class '"ASpliJDU"'
jir Accessors for ASpliJDU object
jir-method Class '"ASpliJDU"'
jir<- Accessors for ASpliJDU object
jir<--method Class '"ASpliJDU"'
joint Accessors for ASpliAS object
joint-method Class '"ASpliAS"'
joint<- Accessors for ASpliAS object
joint<--method Class '"ASpliAS"'
junctionDUreport Differential junction usage estimation
junctionDUreport-method Class '"ASpliCounts"'
junctionsDU Accessors for ASpliDU object
junctionsDU-method Class '"ASpliDU"'
junctionsDU<- Accessors for ASpliDU object
junctionsDU<--method Class '"ASpliDU"'
junctionsPIR Accessors for ASpliAS object
junctionsPIR-method Class '"ASpliAS"'
junctionsPIR<- Accessors for ASpliAS object
junctionsPIR<--method Class '"ASpliAS"'
junctionsPJU Accessors for ASpliAS object
junctionsPJU-method Class '"ASpliAS"'
junctionsPJU<- Accessors for ASpliAS object
junctionsPJU<--method Class '"ASpliAS"'

-- L --

loadBAM Load BAM files
localebased Accessors for ASpliSplicingReport object
localebased-method Class '"ASpliSplicingReport"'
localebased<- Accessors for ASpliSplicingReport object
localebased<--method Class '"ASpliSplicingReport"'
localec Accessors for ASpliJDU object
localec-method Class '"ASpliJDU"'
localec<- Accessors for ASpliJDU object
localec<--method Class '"ASpliJDU"'
localej Accessors for ASpliJDU object
localej-method Class '"ASpliJDU"'
localej<- Accessors for ASpliJDU object
localej<--method Class '"ASpliJDU"'

-- M --

mergeBinDUAS Differential usage of bins and PSI/PIR.
mergeBinDUAS-method Class '"ASpliDU"'

-- P --

plotBins Draw plots of gene counts, bin counts, PSI/PIR value, inclusion and exclusion junctions for selected bins.
plotBins-method Class '"ASpliCounts"'
plotGenomicRegions Create genomic regions coverage plots
plotGenomicRegions-method Class '"ASpliFeatures"'

-- R --

rds Read density of gene and bins
rds-method Class '"ASpliCounts"'
rdsb Accessors for ASpliCounts object
rdsb-method Class '"ASpliCounts"'
rdsb<- Accessors for ASpliCounts object
rdsb<--method Class '"ASpliCounts"'
rdsg Accessors for ASpliCounts object
rdsg-method Class '"ASpliCounts"'
rdsg<- Accessors for ASpliCounts object
rdsg<--method Class '"ASpliCounts"'
readCounts Summarize read overlaps
readCounts-method Class '"ASpliFeatures"'

-- S --

show-method Class '"ASpliIntegratedSignals"'
show-method Class '"ASpliJDU"'
show-method Class '"ASpliSplicingReport"'
show-method Display a summary of data contained in ASpliObjects
show-methods Display a summary of data contained in ASpliObjects
signals Accessors for ASpliIntegratedSignals object
signals-method Class '"ASpliIntegratedSignals"'
signals<- Accessors for ASpliIntegratedSignals object
signals<--method Class '"ASpliIntegratedSignals"'
splicingReport Splicing report
splicingReport-method Class '"ASpliDU"'
splicingReport-method Class '"ASpliIntegratedSignals"'
splicingReport-method Class '"ASpliSplicingReport"'
subset Subset ASpli objects
subset-method Class '"ASpliAS"'
subset-method Class '"ASpliCounts"'
subsetBams Subset ASpli objects
subsetTargets Subset ASpli objects

-- T --

targets Accessors for ASpliCounts object
targets-method Class '"ASpliCounts"'
targets<--method Class '"ASpliCounts"'
transcriptExons Accessors for ASpliFeatures object
transcriptExons-method Class '"ASpliFeatures"'
transcriptExons<- Accessors for ASpliFeatures object
transcriptExons<--method Class '"ASpliFeatures"'

-- W --

writeAll Write results
writeAll-method Class '"ASpliCounts"'
writeAll-method Write results
writeAS Write results
writeAS-method Class '"ASpliAS"'
writeAS-methods Write results
writeCounts Write results
writeCounts-method Class '"ASpliCounts"'
writeCounts-methods Write results
writeDU Write results
writeDU-method Class '"ASpliDU"'
writeDU-methods Write results
writeIntegratedSignals-method Class '"ASpliIntegratedSignals"'
writeJDU Write results
writeJDU-method Class '"ASpliJDU"'
writeJDU-methods Write results
writeRds Write results
writeRds-method Class '"ASpliCounts"'
writeRds-methods Write results
writeSplicingReport Write results
writeSplicingReport-method Class '"ASpliSplicingReport"'
writeSplicingReport-methods Write results