API for PacificBiosciences/R-pbh5
Interface to Pacific Biosciences HDF5 Files

Global functions
$,PacBioCmpH5-method Man page
.NUMBERS Man page
.PAIRS Man page
.bMap Man page
.bMapC Man page
.f Man page
.getAlignmentsWithFeaturesAsDataFrame Man page
.hasDataset Man page
.matchVersion Man page
.ofBasecalls Man page
.ofPulses Man page
H5ObjOrNull-class Man page
MultiPart Source code
PacBioAlnH5 Man page Source code
PacBioAlnH5-class Man page
PacBioBasH5 Man page Source code
PacBioBasH5-class Man page
PacBioCmpH5 Man page Source code
PacBioCmpH5-class Man page
PacBioDataFile-class Man page
PacBioPlsH5 Man page Source code
PacBioPlsH5-class Man page
PacBioTrcH5 Man page Source code
PacBioTrcH5-class Man page
[,PacBioCmpH5,ANY,ANY,ANY-method Man page
alnGroup Man page Source code
alnIndex Man page Source code
applyZMWs Man page Source code
associateWithContext Man page Source code
associateZMWMetric Source code
bMapC Source code
colnames,PacBioCmpH5-method Man page
computeConsensus Man page Source code
computeConsensusRle Source code
convertToLettersFromAscii Source code
convertToSeconds Source code
doByMolecule Source code
doWithPlsAndCmp Man page Source code
doWithPlsAndTrc Man page Source code
geq.1.3.1 Source code
getAccuracy Man page Source code
getAcqParams Man page
getAcqParams,MultiPart-method Man page
getAcqParams,PacBioBasH5-method Man page
getAdvanceTime Man page Source code
getAlignedLength Source code
getAlignmentBlock Man page Source code
getAlignments Man page
getAlignments,PacBioAlnH5-method Man page
getAlignments,PacBioCmpH5-method Man page
getAlignmentsRaw Man page Source code
getAlignmentsWithFeatures Man page Source code
getAlignmentsWithFeaturesAsDataFrame Source code
getAlignmentsWithFeaturesList Source code
getAlnH5String Source code
getBarcodeLabels Man page Source code
getBarcodeMatrix Man page Source code
getBarcodeScores Man page Source code
getBaseEvents Man page
getBaseEvents,MultiPart-method Man page
getBaseEvents,PacBioBasH5-method Man page
getBasecalls Man page Source code
getBaselineLevel Man page
getBaselineLevel,MultiPart-method Man page
getBaselineLevel,PacBioBasH5-method Man page
getBaselineLevel,PacBioPlsH5-method Man page
getBaselineSigma Man page
getBaselineSigma,MultiPart-method Man page
getBaselineSigma,PacBioBasH5-method Man page
getBaselineSigma,PacBioPlsH5-method Man page
getBpzvarw Source code
getByMolecule Source code
getByTemplatePosition Man page Source code
getByTemplatePositionList Source code
getCCSBasecalls Man page Source code
getCallsForReads Man page Source code
getCallsInRange Man page Source code
getChannel Man page Source code
getChannelToBaseMap Man page
getChannelToBaseMap,MultiPart-method Man page
getChannelToBaseMap,PacBioBasH5-method Man page
getChi2 Man page Source code
getClassifierQV Man page
getClassifierQV,PacBioPlsH5-method Man page
getConsensusForIdxs Man page Source code
getConsensusForReads Man page Source code
getConsensusInRange Man page Source code
getCoverageInRange Man page Source code
getCumulativeAdvanceTime Man page Source code
getDatasetByIdx Source code
getDatasetByIdxFast Source code
getDatasetWithChannelCols Source code
getDeletionQV Man page
getDeletionQV,HasBaseAccessors-method Man page
getDeletionQV,PacBioBasH5-method Man page
getDeletionQV,PacBioCmpH5-method Man page
getDeletionTag Man page
getDeletionTag,HasBaseAccessors-method Man page
getDeletionTag,PacBioBasH5-method Man page
getDeletionTag,PacBioCmpH5-method Man page
getEdna Source code
getFrameBasedDataset Source code
getFromBasLikeFile Source code
getFromMultiPartBasLikeFile Source code
getFullRefNames Man page Source code
getHQLength Source code
getHQRegionDuration Source code
getHoleNumbers Man page
getHoleNumbers,MultiPart-method Man page
getHoleNumbers,PacBioBasH5-method Man page
getHoleNumbers,PacBioCmpH5-method Man page
getHoleStatus Source code
getHoleXY Source code
getIPD Man page Source code
getInsertionQV Man page
getInsertionQV,HasBaseAccessors-method Man page
getInsertionQV,PacBioBasH5-method Man page
getInsertionQV,PacBioCmpH5-method Man page
getIsPulse Man page Source code
getKmerContext Man page Source code
getLabelQV Source code
getLocalPolymerizationRate Man page Source code
getMachineName Man page Source code
getMaxSignal Man page Source code
getMeanSignal Man page Source code
getMergeQV Man page
getMergeQV,HasBaseAccessors-method Man page
getMergeQV,PacBioBasH5-method Man page
getMergeQV,PacBioCmpH5-method Man page
getMidSignal Man page Source code
getMidStdDev Source code
getMidStdDevSignal Man page
getMoleculeIndex Man page Source code
getMoleculeIndexList Source code
getMoleculeReadStart Source code
getMovieName Man page
getMovieName,MultiPart-method Man page
getMovieName,PacBioBasH5-method Man page
getMovieName,PacBioCmpH5-method Man page
getNumEvent Man page Source code
getNumEvent,PacBioBasH5-method Man page
getNumEvent,PacBioPlsH5-method Man page
getNumPasses Man page Source code
getParts Source code
getPkmid Man page Source code
getPkmidPhotons Source code
getPkzvarw Source code
getPolymerizationRate Man page Source code
getPreBaseFrames Man page Source code
getPulseEvents Man page
getPulseEvents,MultiPart-method Man page
getPulseEvents,PacBioPlsH5-method Man page
getPulseIndex Man page Source code
getPulseWidth Man page Source code
getQualityValue Man page
getQualityValue,HasBaseAccessors-method Man page
getQualityValue,PacBioBasH5-method Man page
getQualityValue,PacBioCmpH5-method Man page
getQualityValue,PacBioPlsH5-method Man page
getReadEnd Man page Source code
getReadLength Man page Source code
getReadScore Man page
getReadScore,HasBaseAccessors-method Man page
getReadScore,MultiPart-method Man page
getReadScore,PacBioCmpH5-method Man page
getReadStart Man page Source code
getReadType Source code
getReadsInRange Man page Source code
getRefBlock Source code
getRefElt Source code
getRefFullName Man page Source code
getRefLength Man page Source code
getRefMD5 Man page Source code
getRefName Man page Source code
getRefNames Man page Source code
getRefPath Man page Source code
getRegionsTable Man page
getRegionsTable,MultiPart-method Man page
getRegionsTable,PacBioBasH5-method Man page
getRestrictedDataset Source code
getSNR Man page
getSNR,MultiPart-method Man page
getSNR,PacBioBasH5-method Man page Man page
getSNR,PacBioCmpH5-method Man page
getSNR,PacBioPlsH5-method Man page
getStartFrame Man page
getStartFrame,HasBaseAccessors-method Man page
getStartFrame,PacBioBasH5-method Man page
getStartFrame,PacBioCmpH5-method Man page
getStartTime Man page Source code
getSubreadIndex Source code
getSubstitutionQV Man page
getSubstitutionQV,HasBaseAccessors-method Man page
getSubstitutionQV,PacBioBasH5-method Man page
getSubstitutionQV,PacBioCmpH5-method Man page
getSubstitutionTag Man page
getSubstitutionTag,HasBaseAccessors-method Man page
getSubstitutionTag,PacBioBasH5-method Man page
getSubstitutionTag,PacBioCmpH5-method Man page
getTemplateEnd Man page Source code
getTemplatePosition Man page Source code
getTemplateSpan Man page Source code
getTemplateStart Man page Source code
getTemplateStrand Man page Source code
getTraces Man page Source code
getUnrolledReadLength Man page
getUnrolledTemplateSpan Man page Source code
getVersion Man page Source code
getWidthInFrames Man page
getWidthInFrames,HasBaseAccessors-method Man page
getWidthInFrames,PacBioBasH5-method Man page
getWidthInFrames,PacBioPlsH5-method Man page
getZMWs Man page Source code
getZScore Man page Source code
hasAlignmentDataset Source code
head,PacBioCmpH5-method Man page
initialize,PacBioBasH5-method Man page
initialize,PacBioDataFile-method Man page
isMultiPart Source code
isSorted Man page Source code
kMerLabeler Source code
kMerTable Source code
makeContextDataTable Man page Source code
makeKmerLabelCache Source code
makePlsAndTrcProcessor Man page Source code
makeZMWMetricFx Source code
matrixOrNull-class Man page
movieInfo Man page Source code
nFrames Source code
nitBasEvents Source code
nrow,PacBioAlnH5-method Man page
nrow,PacBioCmpH5-method Man page
part Source code
parts Source code
pbh5 Man page
pbh5-package Man page
refGroup Man page Source code
refInfo Man page Source code
restrictCmpH5 Man page Source code
reverse Source code
reverseComplement Source code
show,MultiPart-method Man page
show,PacBioCmpH5-method Man page
show,PacBioDataFile-method Man page
stringOrNull-class Man page
summarizeByContext Man page Source code
summary,PacBioCmpH5-method Man page
templatePositionFromAln Man page Source code
toNA Source code
PacificBiosciences/R-pbh5 documentation built on Oct. 4, 2017, 12:07 a.m.