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

alnIndexGet the AlignmentIndex from a PacBioCmpH5 object
applyZMWsApply Function to ZMWs
doWithPlsAndCmpDo With Pulse And CpmH5
getAlignmentBlockReturns a Specified Alignment Block
getAlignmentsReturn Alignments
getAlignmentsRawReturn Encoded Alignments
getAlignmentsWithFeaturesGet Alignments with Features
getBarcodeLabelsRetrieve Barcode Information from PacBioCmpH5
getBasecallsGet Basecall-level Data From pls.h5 or bas.h5 Files.
getBaseEventsGet Base or Pulse Events
getBaselineSigmaGet Baseline Sigma
getCallsInRangeFunction to get Calls In Range
getChannelPulsecall-level Metrics
getConsensusForIdxsReturn Consensus For Indices
getCoverageInRangeGet Coverage in Range
getCumulativeAdvanceTimeCompute the CumulativeAdvanceTime
getHoleNumbersGet hole numbers Stored in a PacBio HDF5 File.
getIPDCompute the IPD
getLocalPolymerizationRateCompute the local Polymerization Rate
getMachineNameGet machine/movie names.
getNumPassesReturns the number of times a polymerase sequenced the...
getPkmidComputes the Pkmid Values
getPolymerizationRateComputes the Polymerization Rate for each Alignment
getPulseWidthCompute the Pulse Width
getQualityValueReturn Classifier Quality Values
getReadsInRangeRetrieves Reads in Specified Range
getRefPathGet data from refGroup table.
getRegionsTableHigh-level pulse/base file information.
getStartTimeComputes the Start Time of Polymerization
getTemplatePositionGet Position in Template for Aligned Reads
getTemplateSpanFunctions to get information about the alignments.
getTracesGet Traces
getUnrolledTemplateSpanCompute the Unrolled Template Span
getVersionGet Version Information from PacBio HDF5 files
getZMWsGet ZMWs from aln.h5 Files
getZScoreCompute the Z-Score
isSortedFind Out Whether cmpH5 Object is Sorted
makeContextDataTableCompute Statistics Regarding Specific Contexts
PacBioAlnH5-classClass "PacBioAlnH5"
PacBioBasH5-classClass "PacBioBasH5"
PacBioCmpH5-classClass "PacBioCmpH5"
PacBioDataFile-classClass "PacBioDataFile"
PacBioPlsH5-classClass "PacBioPlsH5"
PacBioTrcH5-classClass "PacBioTrcH5"
pbh5-internalInternal pbh5 objects
pbh5-packageInteract with Pacific Biosciences HDF5 Files
restrictCmpH5Limit a cmpH5 to a subset of the reads.
PacificBiosciences/R-pbh5 documentation built on Oct. 4, 2017, 12:07 a.m.