alnIndex: Get the AlignmentIndex from a PacBioCmpH5 object

In PacificBiosciences/R-pbh5: Interface to Pacific Biosciences HDF5 Files

Description

'alnIndex' returns the alignment index from a PacBioCmpH5 object, including information about ID, alnGroupPath, movieName, refName, tStart, tEnd, alignedStrand, holeNumber, setNumber, strobeNumber, moleculeID, rStart, rEnd, mapQV, nMatches, nMisMatches, nInsertions, ndeletions, offsetBegin, offsetEnd, nBackRead and nOverlap.

Usage

  alnIndex(cmpH5)

Arguments

cmpH5

An object of class PacBioCmpH5

Value

'alnIndex' returns a data.frame where each row represents an alignment, and each column represents unique information about the alignment. 'alnGroup' returns a data.frame where each row is a unique Path. See description.

See Also

PacBioCmpH5-class

Examples

  require(pbh5)
  cmpH5 <- PacBioCmpH5(system.file("h5_files",  "aligned_reads.cmp.h5",
  package = "pbh5"))
  alignments <- alnIndex(cmpH5)
  class(alignments)
  head(alignments)
  alignGroup <-alnGroup(cmpH5)
  head(alignGroup)

PacificBiosciences/R-pbh5 documentation built on May 7, 2019, 11:54 p.m.