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
PacBioAlnH5	Man page
PacBioAlnH5-class	Man page
PacBioBasH5	Man page
PacBioBasH5-class	Man page
PacBioCmpH5	Man page
PacBioCmpH5-class	Man page
PacBioDataFile-class	Man page
PacBioPlsH5	Man page
PacBioPlsH5-class	Man page
PacBioTrcH5	Man page
PacBioTrcH5-class	Man page
[,PacBioCmpH5,ANY,ANY,ANY-method	Man page
alnGroup	Man page
alnIndex	Man page
applyZMWs	Man page
associateWithContext	Man page
colnames,PacBioCmpH5-method	Man page
computeConsensus	Man page
doWithPlsAndCmp	Man page
doWithPlsAndTrc	Man page
getAccuracy	Man page
getAcqParams	Man page
getAcqParams,MultiPart-method	Man page
getAcqParams,PacBioBasH5-method	Man page
getAdvanceTime	Man page
getAlignmentBlock	Man page
getAlignments	Man page
getAlignments,PacBioAlnH5-method	Man page
getAlignments,PacBioCmpH5-method	Man page
getAlignmentsRaw	Man page
getAlignmentsWithFeatures	Man page
getBarcodeLabels	Man page
getBarcodeMatrix	Man page
getBarcodeScores	Man page
getBaseEvents	Man page
getBaseEvents,MultiPart-method	Man page
getBaseEvents,PacBioBasH5-method	Man page
getBasecalls	Man page
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
getByTemplatePosition	Man page
getCCSBasecalls	Man page
getCallsForReads	Man page
getCallsInRange	Man page
getChannel	Man page
getChannelToBaseMap	Man page
getChannelToBaseMap,MultiPart-method	Man page
getChannelToBaseMap,PacBioBasH5-method	Man page
getChi2	Man page
getClassifierQV	Man page
getClassifierQV,PacBioPlsH5-method	Man page
getConsensusForIdxs	Man page
getConsensusForReads	Man page
getConsensusInRange	Man page
getCoverageInRange	Man page
getCumulativeAdvanceTime	Man page
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
getFullRefNames	Man page
getHoleNumbers	Man page
getHoleNumbers,MultiPart-method	Man page
getHoleNumbers,PacBioBasH5-method	Man page
getHoleNumbers,PacBioCmpH5-method	Man page
getIPD	Man page
getInsertionQV	Man page
getInsertionQV,HasBaseAccessors-method	Man page
getInsertionQV,PacBioBasH5-method	Man page
getInsertionQV,PacBioCmpH5-method	Man page
getIsPulse	Man page
getKmerContext	Man page
getLocalPolymerizationRate	Man page
getMachineName	Man page
getMaxSignal	Man page
getMeanSignal	Man page
getMergeQV	Man page
getMergeQV,HasBaseAccessors-method	Man page
getMergeQV,PacBioBasH5-method	Man page
getMergeQV,PacBioCmpH5-method	Man page
getMidSignal	Man page
getMidStdDevSignal	Man page
getMoleculeIndex	Man page
getMovieName	Man page
getMovieName,MultiPart-method	Man page
getMovieName,PacBioBasH5-method	Man page
getMovieName,PacBioCmpH5-method	Man page
getNumEvent	Man page
getNumEvent,PacBioBasH5-method	Man page
getNumEvent,PacBioPlsH5-method	Man page
getNumPasses	Man page
getPkmid	Man page
getPolymerizationRate	Man page
getPreBaseFrames	Man page
getPulseEvents	Man page
getPulseEvents,MultiPart-method	Man page
getPulseEvents,PacBioPlsH5-method	Man page
getPulseIndex	Man page
getPulseWidth	Man page
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
getReadLength	Man page
getReadScore	Man page
getReadScore,HasBaseAccessors-method	Man page
getReadScore,MultiPart-method	Man page
getReadScore,PacBioCmpH5-method	Man page
getReadStart	Man page
getReadsInRange	Man page
getRefFullName	Man page
getRefLength	Man page
getRefMD5	Man page
getRefName	Man page
getRefNames	Man page
getRefPath	Man page
getRegionsTable	Man page
getRegionsTable,MultiPart-method	Man page
getRegionsTable,PacBioBasH5-method	Man page
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
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
getTemplatePosition	Man page
getTemplateSpan	Man page
getTemplateStart	Man page
getTemplateStrand	Man page
getTraces	Man page
getUnrolledReadLength	Man page
getUnrolledTemplateSpan	Man page
getVersion	Man page
getWidthInFrames	Man page
getWidthInFrames,HasBaseAccessors-method	Man page
getWidthInFrames,PacBioBasH5-method	Man page
getWidthInFrames,PacBioPlsH5-method	Man page
getZMWs	Man page
getZScore	Man page
head,PacBioCmpH5-method	Man page
initialize,PacBioBasH5-method	Man page
initialize,PacBioDataFile-method	Man page
isSorted	Man page
makeContextDataTable	Man page
makePlsAndTrcProcessor	Man page
matrixOrNull-class	Man page
movieInfo	Man page
nrow,PacBioAlnH5-method	Man page
nrow,PacBioCmpH5-method	Man page
pbh5	Man page
pbh5-package	Man page
refGroup	Man page
refInfo	Man page
restrictCmpH5	Man page
show,MultiPart-method	Man page
show,PacBioCmpH5-method	Man page
show,PacBioDataFile-method	Man page
stringOrNull-class	Man page
summarizeByContext	Man page
summary,PacBioCmpH5-method	Man page
templatePositionFromAln	Man page