Man pages for PacificBiosciences/R-pbh5
Interface to Pacific Biosciences HDF5 Files
| alnIndex | Get the AlignmentIndex from a PacBioCmpH5 object |
| applyZMWs | Apply Function to ZMWs |
| doWithPlsAndCmp | Do With Pulse And CpmH5 |
| getAlignmentBlock | Returns a Specified Alignment Block |
| getAlignments | Return Alignments |
| getAlignmentsRaw | Return Encoded Alignments |
| getAlignmentsWithFeatures | Get Alignments with Features |
| getBarcodeLabels | Retrieve Barcode Information from PacBioCmpH5 |
| getBasecalls | Get Basecall-level Data From pls.h5 or bas.h5 Files. |
| getBaseEvents | Get Base or Pulse Events |
| getBaselineSigma | Get Baseline Sigma |
| getCallsInRange | Function to get Calls In Range |
| getChannel | Pulsecall-level Metrics |
| getConsensusForIdxs | Return Consensus For Indices |
| getCoverageInRange | Get Coverage in Range |
| getCumulativeAdvanceTime | Compute the CumulativeAdvanceTime |
| getHoleNumbers | Get hole numbers Stored in a PacBio HDF5 File. |
| getIPD | Compute the IPD |
| getLocalPolymerizationRate | Compute the local Polymerization Rate |
| getMachineName | Get machine/movie names. |
| getNumPasses | Returns the number of times a polymerase sequenced the... |
| getPkmid | Computes the Pkmid Values |
| getPolymerizationRate | Computes the Polymerization Rate for each Alignment |
| getPulseWidth | Compute the Pulse Width |
| getQualityValue | Return Classifier Quality Values |
| getReadsInRange | Retrieves Reads in Specified Range |
| getRefPath | Get data from refGroup table. |
| getRegionsTable | High-level pulse/base file information. |
| getStartTime | Computes the Start Time of Polymerization |
| getTemplatePosition | Get Position in Template for Aligned Reads |
| getTemplateSpan | Functions to get information about the alignments. |
| getTraces | Get Traces |
| getUnrolledTemplateSpan | Compute the Unrolled Template Span |
| getVersion | Get Version Information from PacBio HDF5 files |
| getZMWs | Get ZMWs from aln.h5 Files |
| getZScore | Compute the Z-Score |
| isSorted | Find Out Whether cmpH5 Object is Sorted |
| makeContextDataTable | Compute Statistics Regarding Specific Contexts |
| PacBioAlnH5-class | Class "PacBioAlnH5" |
| PacBioBasH5-class | Class "PacBioBasH5" |
| PacBioCmpH5-class | Class "PacBioCmpH5" |
| PacBioDataFile-class | Class "PacBioDataFile" |
| PacBioPlsH5-class | Class "PacBioPlsH5" |
| PacBioTrcH5-class | Class "PacBioTrcH5" |
| pbh5-internal | Internal pbh5 objects |
| pbh5-package | Interact with Pacific Biosciences HDF5 Files |
| restrictCmpH5 | Limit a cmpH5 to a subset of the reads. |
