API for ASpli
Analysis of Alternative Splicing Using RNA-Seq

Global functions
.DUReportBins	Source code
.DUReportBinsWithDiffSplice	Source code
.DUreport	Source code
.arrangeLayout	Source code
.binsDUWithDiffSplice	Source code
.binsJDUWithDiffSplice	Source code
.countJbyCondition	Source code
.counterBin	Source code
.counterGenes	Source code
.counterJbin	Source code
.counterJunctions	Source code
.createGRangesExons	Source code
.createGRangesExpJunctions	Source code
.createGRangesGenes	Source code
.createGRangesIntrons	Source code
.createGRangesJunctions	Source code
.createGRangesTranscripts	Source code
.definePlottingRegions	Source code
.e1e2JPIR	Source code
.edgeRtest	Source code
.evaluateByGroup	Source code
.filter.ASpliDU	Source code
.filterBins	Source code
.filterByGeneric	Source code
.filterByGroup	Source code
.filterByRdBinRATIO	Source code
.filterByRdGen	Source code
.filterByReads	Source code
.filterGenes	Source code
.filterJunctionBySample	Source code
.filterJunctionBySampleWithContrast	Source code
.filterReadCounts	Source code
.filterSignals	Source code
.findAsBin	Source code
.genesDE	Source code
.getBamMatrix	Source code
.getExpFactors	Source code
.getGeneGRanges	Source code
.getJunctionMatchingBins	Source code
.getJunctionOverlapGeneData	Source code
.getJunctionSpanningBins	Source code
.getJunctionWithinBins	Source code
.getOffsetMatrix	Source code
.integrateSignals	Source code
.junctionDUreportExt	Source code
.junctionsDU_SUM	Source code
.junctionsDiscover	Source code
.junctionsPSI_SUM	Source code
.makeClusters	Source code
.makeCountData	Source code
.makeCountDataWithClusters	Source code
.makeJunctions	Source code
.makeLegends	Source code
.makeReduxData	Source code
.makeValidFileName	Source code
.makeXticksLabels	Source code
.meanLogCPMIs	Source code
.mergeBinDUAS	Source code
.my_replace_na	Source code
.normalizeByGenFeature	Source code
.ovBinJunction	Source code
.plotASpliDetectionSummary	Source code
.plotBars	Source code
.plotBins	Source code
.plotGenomicRegions	Source code
.plotSingleBin	Source code
.plotSplicingPattern	Source code
.plotSplicingPattern.orig	Source code
.prepareData	Source code
.splicingReport	Source code
.subset.ASpliAS	Source code
.subset.ASpliCounts	Source code
.sumByCond	Source code
.testUniformity	Source code
ASpli	Man page
ASpli-deprecated	Man page
ASpli-package	Man page
ASpliAS	Man page
ASpliAS-class	Man page
ASpliCounts	Man page
ASpliCounts-class	Man page
ASpliDU	Man page
ASpliDU-class	Man page
ASpliFeatures-class	Man page
ASpliIntegratedSignals	Man page
ASpliIntegratedSignals-class	Man page
ASpliJDU	Man page
ASpliJDU-class	Man page
ASpliSplicingReport	Man page
ASpliSplicingReport-class	Man page
AsDiscover	Man page
AsDiscover,ASpliCounts-method	Man page
DUreport	Man page
DUreport,ASpliCounts-method	Man page
DUreport.norm	Man page
DUreport.norm,ASpliCounts-method	Man page
DUreport.offset	Man page
DUreport.offset,ASpliCounts-method	Man page
DUreportBinSplice	Man page
DUreportBinSplice,ASpliCounts-method	Man page
altPSI	Man page
altPSI,ASpliAS-method	Man page
altPSI<-	Man page
altPSI<-,ASpliAS,data.frame-method	Man page
anchorbased	Man page
anchorbased,ASpliSplicingReport-method	Man page
anchorbased<-	Man page
anchorbased<-,ASpliSplicingReport,data.frame-method	Man page
anchorc	Man page
anchorc,ASpliJDU-method	Man page
anchorc<-	Man page
anchorc<-,ASpliJDU,data.frame-method	Man page
anchorj	Man page
anchorj,ASpliJDU-method	Man page
anchorj<-	Man page
anchorj<-,ASpliJDU,data.frame-method	Man page
aspliASexample	Man page Source code
aspliBamsExample	Man page Source code
aspliCountsExample	Man page Source code
aspliDUexample1	Man page Source code
aspliDUexample2	Man page Source code
aspliExampleBamList	Man page Source code
aspliExampleGTF	Man page Source code
aspliFeaturesExample	Man page Source code
aspliJunctionDUexample	Man page Source code
aspliTargetsExample	Man page Source code
binGenome	Man page
binGenome,TxDb-method	Man page
binGenome-methods	Man page
binbased	Man page
binbased,ASpliSplicingReport-method	Man page
binbased<-	Man page
binbased<-,ASpliSplicingReport,data.frame-method	Man page
binsDU	Man page
binsDU,ASpliDU-method	Man page
binsDU<-	Man page
binsDU<-,ASpliDU-method	Man page
condition.order	Man page
condition.order,ASpliCounts-method	Man page
containsGenesAndBins	Man page
containsGenesAndBins,ASpliDU-method	Man page
containsJunctions	Man page
containsJunctions,ASpliDU-method	Man page
countsb	Man page
countsb,ASpliCounts-method	Man page
countsb<-	Man page
countsb<-,ASpliCounts,data.frame-method	Man page
countse1i	Man page
countse1i,ASpliCounts-method	Man page
countse1i<-	Man page
countse1i<-,ASpliCounts,data.frame-method	Man page
countsg	Man page
countsg,ASpliCounts-method	Man page
countsg<-	Man page
countsg<-,ASpliCounts,data.frame-method	Man page
countsie2	Man page
countsie2,ASpliCounts-method	Man page
countsie2<-	Man page
countsie2<-,ASpliCounts,data.frame-method	Man page
countsj	Man page
countsj,ASpliCounts-method	Man page
countsj<-	Man page
countsj<-,ASpliCounts,data.frame-method	Man page
esPSI	Man page
esPSI,ASpliAS-method	Man page
esPSI<-	Man page
esPSI<-,ASpliAS,data.frame-method	Man page
exportIntegratedSignals	Man page
exportIntegratedSignals,ASpliIntegratedSignals-method	Man page
exportSplicingReports	Man page
exportSplicingReports,ASpliSplicingReport-method	Man page
featuresb	Man page
featuresb,ASpliFeatures-method	Man page
featuresb<-	Man page
featuresb<-,ASpliFeatures,GRanges-method	Man page
featuresg	Man page
featuresg,ASpliFeatures-method	Man page
featuresg<-	Man page
featuresg<-,ASpliFeatures,GRangesList-method	Man page
featuresj	Man page
featuresj,ASpliFeatures-method	Man page
featuresj<-	Man page
featuresj<-,ASpliFeatures,GRanges-method	Man page
filterDU	Man page
filterDU,ASpliDU-method	Man page
filterSignals	Man page
filterSignals,ASpliSplicingReport-method	Man page
filters	Man page
filters,ASpliIntegratedSignals-method	Man page
filters<-	Man page
filters<-,ASpliIntegratedSignals,data.frame-method	Man page
gbCounts	Man page
gbCounts,ASpliFeatures-method	Man page
gbDUreport	Man page
gbDUreport,ASpliCounts-method	Man page
genesDE	Man page
genesDE,ASpliDU-method	Man page
genesDE<-	Man page
genesDE<-,ASpliDU,data.frame-method	Man page
getConditions	Man page Source code
integrateSignals	Man page
integrateSignals,ASpliSplicingReport-method	Man page
irPIR	Man page
irPIR,ASpliAS-method	Man page
irPIR<-	Man page
irPIR<-,ASpliAS,data.frame-method	Man page
jCounts	Man page
jCounts,ASpliCounts-method	Man page
jDUreport	Man page
jDUreport,ASpliAS-method	Man page
jDUreport,ASpliJDU-method	Man page
jalt	Man page
jalt,ASpliJDU-method	Man page
jalt<-	Man page
jalt<-,ASpliJDU,data.frame-method	Man page
jes	Man page
jes,ASpliJDU-method	Man page
jes<-	Man page
jes<-,ASpliJDU,data.frame-method	Man page
jir	Man page
jir,ASpliJDU-method	Man page
jir<-	Man page
jir<-,ASpliJDU,data.frame-method	Man page
joint	Man page
joint,ASpliAS-method	Man page
joint<-	Man page
joint<-,ASpliAS,data.frame-method	Man page
junctionDUreport	Man page
junctionDUreport,ASpliCounts-method	Man page
junctionsDU	Man page
junctionsDU,ASpliDU-method	Man page
junctionsDU<-	Man page
junctionsDU<-,ASpliDU,data.frame-method	Man page
junctionsPIR	Man page
junctionsPIR,ASpliAS-method	Man page
junctionsPIR<-	Man page
junctionsPIR<-,ASpliAS,data.frame-method	Man page
junctionsPJU	Man page
junctionsPJU,ASpliAS-method	Man page
junctionsPJU<-	Man page
junctionsPJU<-,ASpliAS,data.frame-method	Man page
loadBAM	Man page Source code
localebased	Man page
localebased,ASpliSplicingReport-method	Man page
localebased<-	Man page
localebased<-,ASpliSplicingReport,data.frame-method	Man page
localec	Man page
localec,ASpliJDU-method	Man page
localec<-	Man page
localec<-,ASpliJDU,data.frame-method	Man page
localej	Man page
localej,ASpliJDU-method	Man page
localej<-	Man page
localej<-,ASpliJDU,data.frame-method	Man page
mergeBinDUAS	Man page
mergeBinDUAS,ASpliDU,ASpliAS-method	Man page
plotBins	Man page
plotBins,ASpliCounts-method	Man page
plotGenomicRegions	Man page
plotGenomicRegions,ASpliFeatures-method	Man page
rds	Man page
rds,ASpliCounts-method	Man page
rdsb	Man page
rdsb,ASpliCounts-method	Man page
rdsb<-	Man page
rdsb<-,ASpliCounts,data.frame-method	Man page
rdsg	Man page
rdsg,ASpliCounts-method	Man page
rdsg<-	Man page
rdsg<-,ASpliCounts,data.frame-method	Man page
readCounts	Man page
readCounts,ASpliFeatures-method	Man page
show,ASpliAS-method	Man page
show,ASpliCounts-method	Man page
show,ASpliDU-method	Man page
show,ASpliFeatures-method	Man page
show,ASpliIntegratedSignals-method	Man page
show,ASpliJDU-method	Man page
show,ASpliMergedReports-method	Man page
show,ASpliSplicingReport-method	Man page
show-methods	Man page
signals	Man page
signals,ASpliIntegratedSignals-method	Man page
signals<-	Man page
signals<-,ASpliIntegratedSignals,data.frame-method	Man page
splicingReport	Man page
splicingReport,ASpliDU-method	Man page
splicingReport,ASpliIntegratedSignals-method	Man page
splicingReport,ASpliSplicingReport-method	Man page
subset	Man page
subset,ASpliAS-method	Man page
subset,ASpliCounts-method	Man page
subsetBams	Man page Source code
subsetTargets	Man page Source code
targets	Man page
targets,ASpliCounts-method	Man page
targets<-,ASpliCounts,data.frame-method	Man page
transcriptExons	Man page
transcriptExons,ASpliFeatures-method	Man page
transcriptExons<-	Man page
transcriptExons<-,ASpliFeatures,GRangesList-method	Man page
writeAS	Man page
writeAS,ASpliAS-method	Man page
writeAS-methods	Man page
writeAll	Man page
writeAll,ANY-method	Man page
writeAll,ASpliCounts-method	Man page
writeCounts	Man page
writeCounts,ASpliCounts-method	Man page
writeCounts-methods	Man page
writeDU	Man page
writeDU,ASpliDU-method	Man page
writeDU-methods	Man page
writeIntegratedSignals,ASpliIntegratedSignals-method	Man page
writeJDU	Man page
writeJDU,ASpliJDU-method	Man page
writeJDU-methods	Man page
writeRds	Man page
writeRds,ASpliCounts-method	Man page
writeRds-methods	Man page
writeSplicingReport	Man page
writeSplicingReport,ASpliSplicingReport-method	Man page
writeSplicingReport-methods	Man page