API for SGSeq
Splice event prediction and quantification from RNA-seq data

Global functions
FPKM	Man page
FPKM,SGFeatureCounts-method	Man page
FPKM,SGVariantCounts-method	Man page
FPKM<-	Man page
FPKM<-,SGFeatureCounts-method	Man page
SGFeatureCounts	Man page Source code
SGFeatures	Man page Source code
SGSegments	Man page Source code
SGVariantCounts	Man page Source code
SGVariants	Man page Source code
TxFeatures	Man page Source code
XS2strand	Source code
addAlpha	Source code
addDummyNodes	Source code
addDummySpliceSites	Source code
addFeatureID	Source code
addGeneID	Source code
addSourceAndSinkNodes	Source code
addSpliceSites	Source code
analyzeFeatures	Man page Source code
analyzeVariants	Man page Source code
annotate	Man page Source code
annotateFeatures	Source code
annotatePaths	Source code
annotateSGVariants	Man page Source code
annotateSegments	Source code
asGRanges	Source code
asGRangesList	Source code
assays	Man page
calculateSizeFactor	Source code
cds	Source code
cdsEnd	Source code
cdsLeft	Source code
cdsRight	Source code
cdsStart	Source code
checkApplyResultsForErrors	Source code
checkBamInfo	Source code
checkIdenticalSummarizedExperiment	Source code
checkSampleInfo	Source code
checkTranscriptFormat	Source code
closed3p	Man page
closed3p,SGVariantCounts-method	Man page
closed3p,SGVariants-method	Man page
closed3p<-	Man page
closed3p<-,SGVariantCounts-method	Man page
closed3p<-,SGVariants-method	Man page
closed3pEvent	Man page
closed3pEvent,SGVariantCounts-method	Man page
closed3pEvent,SGVariants-method	Man page
closed3pEvent<-	Man page
closed3pEvent<-,SGVariantCounts-method	Man page
closed3pEvent<-,SGVariants-method	Man page
closed5p	Man page
closed5p,SGVariantCounts-method	Man page
closed5p,SGVariants-method	Man page
closed5p<-	Man page
closed5p<-,SGVariantCounts-method	Man page
closed5p<-,SGVariants-method	Man page
closed5pEvent	Man page
closed5pEvent,SGVariantCounts-method	Man page
closed5pEvent,SGVariants-method	Man page
closed5pEvent<-	Man page
closed5pEvent<-,SGVariantCounts-method	Man page
closed5pEvent<-,SGVariants-method	Man page
co2gr	Source code
co2str	Source code
collapseFeatures	Source code
collapseRows	Source code
completeMcols	Source code
constructGRangesFromRanges	Source code
convertFpkmToCount	Source code
convertSlots	Source code
convertToSGFeatures	Man page Source code
convertToSGSegments	Source code
convertToTranscripts	Source code
convertToTxFeatures	Man page Source code
counts,SGFeatureCounts-method	Man page
counts,SGVariantCounts-method	Man page
counts<-,SGFeatureCounts-method	Man page
counts<-,SGVariantCounts-method	Man page
createSGFeaturesFromSGVariants	Source code
dropMcols	Source code
edges	Source code
eventID	Man page
eventID,SGVariantCounts-method	Man page
eventID,SGVariants-method	Man page
eventID<-	Man page
eventID<-,SGVariantCounts-method	Man page
eventID<-,SGVariants-method	Man page
exonCompatible	Man page Source code
exonCoverage	Source code
exonFrame	Source code
exonGraph	Source code
exonGraphEdges	Source code
exonGraphNodes	Source code
exonsOnSameChromAndStrand	Source code
expandSGVariantCounts	Source code
expandString	Source code
expandType	Source code
expandUnstrandedRanges	Source code
exportFeatures	Man page Source code
extractExons	Source code
extractFeaturesFromVariants	Source code
extractIDs	Source code
extractJunctions	Source code
extractRangesFromFeatures	Source code
extractSplicesitesFromJunctions	Source code
feature2name	Source code
featureID	Man page
featureID,Counts-method	Man page
featureID,Paths-method	Man page
featureID,SGFeatures-method	Man page
featureID3p	Man page
featureID3p,SGVariantCounts-method	Man page
featureID3p,SGVariants-method	Man page
featureID3p<-	Man page
featureID3p<-,SGVariantCounts-method	Man page
featureID3p<-,SGVariants-method	Man page
featureID3pEvent	Man page
featureID3pEvent,SGVariantCounts-method	Man page
featureID3pEvent,SGVariants-method	Man page
featureID3pEvent<-	Man page
featureID3pEvent<-,SGVariantCounts-method	Man page
featureID3pEvent<-,SGVariants-method	Man page
featureID5p	Man page
featureID5p,SGVariantCounts-method	Man page
featureID5p,SGVariants-method	Man page
featureID5p<-	Man page
featureID5p<-,SGVariantCounts-method	Man page
featureID5p<-,SGVariants-method	Man page
featureID5pEvent	Man page
featureID5pEvent,SGVariantCounts-method	Man page
featureID5pEvent,SGVariants-method	Man page
featureID5pEvent<-	Man page
featureID5pEvent<-,SGVariantCounts-method	Man page
featureID5pEvent<-,SGVariants-method	Man page
featureID<-	Man page
featureID<-,Counts-method	Man page
featureID<-,Paths-method	Man page
featureID<-,SGFeatures-method	Man page
filterExonsInternal	Source code
filterExonsTerminal	Source code
filterFeatures	Man page Source code
filterGa	Source code
filterGap	Source code
filterIntrons	Source code
filterJunctions	Source code
findAllPaths	Source code
findCDS	Source code
findEvents	Source code
findOverlapsRanges	Man page Source code
findSGSegments	Source code
findSGSegmentsPerGene	Source code
findSGVariants	Man page Source code
findSGVariantsFromSGFeatures	Source code
findVariantsPerGene	Source code
from,Paths-method	Man page
from,SGVariantCounts-method	Man page
from<-	Man page
from<-,Paths-method	Man page
from<-,SGVariantCounts-method	Man page
geneID	Man page
geneID,Counts-method	Man page
geneID,Paths-method	Man page
geneID,SGFeatures-method	Man page
geneID<-	Man page
geneID<-,Counts-method	Man page
geneID<-,Paths-method	Man page
geneID<-,SGFeatures-method	Man page
geneName	Man page
geneName,Counts-method	Man page
geneName,Features-method	Man page
geneName,Paths-method	Man page
geneName<-	Man page
geneName<-,Counts-method	Man page
geneName<-,Features-method	Man page
geneName<-,Paths-method	Man page
generateCompleteMessage	Source code
generateWarningMessage	Source code
getBamInfo	Man page Source code
getBamInfoPerSample	Source code
getCoverage	Source code
getCoveragePerSample	Source code
getEffectiveLengths	Source code
getEventLocation	Source code
getExonCoordinates	Source code
getFeatureLengths	Source code
getGraphInfo	Source code
getHGVSDeletion	Source code
getHGVSFlanking	Source code
getHGVSInsertion	Source code
getHGVSRefPos	Source code
getHGVSRefPosIntronic	Source code
getHGVSVariantDeletionInsertion	Source code
getHGVSVariantFrameshift	Source code
getHGVSVariantNTerminalExtension	Source code
getHGVSVariantNTerminalVariant	Source code
getHGVSVariantNoProtein	Source code
getHGVSVariantProteinUnaffected	Source code
getHGVSVariantRNA	Source code
getLayoutParameters	Source code
getPadding	Source code
getProteinSeq	Source code
getRNASeq	Source code
getRepresentativeFeatureIDs	Source code
getSGFeatureCounts	Man page Source code
getSGFeatureCountsPerSample	Man page Source code
getSGFeatureCountsPerStrand	Source code
getSGVariantCounts	Man page Source code
getSGVariantCountsFromBamFiles	Source code
getSGVariantCountsFromSGFeatureCounts	Source code
getSGVariantCountsPerSample	Source code
getSGVariantCountsPerStrand	Source code
getScaledCounts	Source code
getTerminalFeatureIDs	Source code
getVariant	Source code
getVariantFreq	Source code
getVariantProtein	Source code
getVariantRNA	Source code
gr	Man page
gr2co	Source code
gr2pos	Source code
importTranscripts	Man page Source code
isOr	Source code
junctionCompatible	Man page Source code
makeCompleteMessage	Source code
makeErrorMessage	Source code
makeSGFeatureCounts	Man page Source code
makeSGVariantCounts	Source code
makeVariantNames	Man page Source code
makeWarningMessage	Source code
mapEventToProtein	Source code
mapVariantsToTranscripts	Source code
maskInnerEvents	Source code
matchExon	Source code
matchJunction	Source code
matchSGFeatures	Source code
matchSplice	Source code
matchTxFeatures	Source code
mergeExonsTerminal	Source code
mergeSGFeatures	Source code
mergeTxFeatures	Man page Source code
neighborhood2	Source code
nextFrame	Source code
nodes	Source code
pfirst	Source code
pintersect	Source code
plast	Source code
plotCoverage	Man page Source code
plotExonGraph	Source code
plotFeatures	Man page Source code
plotImage	Source code
plotRanges	Source code
plotSpliceGraph	Man page Source code
plotTrackRanges	Source code
plotTrackScore	Source code
plotVariants	Man page Source code
pos2gr	Source code
pos2str	Source code
predictCandidatesInternal	Man page Source code
predictCandidatesTerminal	Man page Source code
predictExonsInternal	Man page Source code
predictExonsTerminal	Man page Source code
predictJunctions	Man page Source code
predictSpliced	Man page Source code
predictTxFeatures	Man page Source code
predictTxFeaturesPerSample	Man page Source code
predictTxFeaturesPerStrand	Man page Source code
predictVariantEffectPerVariantAndTranscript	Source code
predictVariantEffects	Man page Source code
processFeatures	Source code
processTerminalExons	Man page Source code
processTranscripts	Source code
propagateAnnotation	Source code
propagateXS	Source code
punion	Source code
rbindDfsWithoutRowNames	Source code
rbindListOfDFs	Source code
readGap	Source code
reindex	Source code
removeExonsIsolated	Man page Source code
reorderFeatures	Source code
restrictFeatures	Source code
scorePerExon	Source code
segmentID	Man page
segmentID,Paths-method	Man page
segmentID,SGVariantCounts-method	Man page
segmentID<-	Man page
segmentID<-,Paths-method	Man page
segmentID<-,SGVariantCounts-method	Man page
selectFeatures	Source code
setCores	Source code
setFeatureColors	Source code
setPreschedule	Source code
sgf_ann	Man page
sgf_pred	Man page
sgfc_ann	Man page
sgfc_pred	Man page
sgv_ann	Man page
sgv_pred	Man page
sgvc_ann	Man page
sgvc_ann_from_bam	Man page
sgvc_pred	Man page
sgvc_pred_from_bam	Man page
si	Man page
silent_select	Source code
slots	Man page
sortEvents	Source code
splice3p	Man page
splice3p,SGFeatureCounts-method	Man page
splice3p,SGFeatures-method	Man page
splice3p,SGSegments-method	Man page
splice3p<-	Man page
splice3p<-,SGFeatureCounts-method	Man page
splice3p<-,SGFeatures-method	Man page
splice3p<-,SGSegments-method	Man page
splice5p	Man page
splice5p,SGFeatureCounts-method	Man page
splice5p,SGFeatures-method	Man page
splice5p,SGSegments-method	Man page
splice5p<-	Man page
splice5p<-,SGFeatureCounts-method	Man page
splice5p<-,SGFeatures-method	Man page
splice5p<-,SGSegments-method	Man page
spliceGraph	Source code
splicesiteCounts	Source code
splicesiteOverlap	Man page Source code
splitCharacterList	Source code
subgraph	Source code
to,Paths-method	Man page
to,SGVariantCounts-method	Man page
to<-	Man page
to<-,Paths-method	Man page
to<-,SGVariantCounts-method	Man page
tx	Man page
txName	Man page
txName,Counts-method	Man page
txName,Features-method	Man page
txName,Paths-method	Man page
txName<-	Man page
txName<-,Counts-method	Man page
txName<-,Features-method	Man page
txName<-,Paths-method	Man page
txf_ann	Man page
txf_pred	Man page
type,Counts-method	Man page
type,Features-method	Man page
type,Paths-method	Man page
type<-	Man page
type<-,Counts-method	Man page
type<-,Features-method	Man page
type<-,Paths-method	Man page
typeLevels	Source code
uniqueFeatures	Source code
unmaskEvents	Source code
updateObject	Man page
updateObject,SGVariantCounts-method	Man page
updateObject,SGVariants-method	Man page
validAssays	Source code
validExtraColumnSlotLengths	Source code
validExtraColumnSlotValues	Source code
validMcols	Source code
validSGFeatureCounts	Source code
validSGFeatures	Source code
validSGSegments	Source code
validSGVariantCounts	Source code
validSGVariants	Source code
validTxFeatures	Source code
validValues	Source code
variantFreq	Man page
variantFreq,SGVariantCounts-method	Man page
variantFreq<-	Man page
variantFreq<-,SGVariantCounts-method	Man page
variantID	Man page
variantID,SGVariantCounts-method	Man page
variantID,SGVariants-method	Man page
variantID<-	Man page
variantID<-,SGVariantCounts-method	Man page
variantID<-,SGVariants-method	Man page
variantName	Man page
variantName,SGVariantCounts-method	Man page
variantName,SGVariants-method	Man page
variantName<-	Man page
variantName<-,SGVariantCounts-method	Man page
variantName<-,SGVariants-method	Man page
variantType	Man page
variantType,SGVariantCounts-method	Man page
variantType,SGVariants-method	Man page
variantType<-	Man page
variantType<-,SGVariantCounts-method	Man page
variantType<-,SGVariants-method	Man page
xcoordinates	Source code