# Analysis of Alternative Splicing Using RNA-Seq

## Documentation for package ‘ASpli’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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