getQualityValue: Return Classifier Quality Values
In PacificBiosciences/R-pbh5: Interface to Pacific Biosciences HDF5 Files

Description Usage Arguments Details Value Examples

Return classifier quality values from a class/file which contains them.

  getQualityValue(h5Obj, ...)
  getInsertionQV(h5Obj, ...)
  getDeletionQV(h5Obj, ...)
  getMergeQV(h5Obj, ...)
  getSubstitutionQV(h5Obj, ...)

  getDeletionTag(h5Obj, ...)
  getSubstitutionTag(h5Obj, ...)

`h5Obj`	An object of class `PacBioCmpH5-class` or `PacBioBasH5-class`
`...`	Extra arguments – See class documentation for `h5Obj`

Quality values are provided in the standard phred scaling,

QV = -10 \log_{10} p_{err}

so that a larger QV values indicates a smaller probability of the given error type.

Deletion QVs correspond to the the probability of a deletion event occuring before the indicated sequence position, and the DeletionTag value will be an uppercase ASCII-encoded DNA base (‘A’, ‘C’, ‘T’, ‘G’) or else ‘N’ if the primary pipeline did not identify a "most-likely" deleted base.

Quality values are calculated in the primary analysis pipeline based on pulse metrics.

A list of vectors of quality values.

  gc()
  require(pbh5)
  cmpH5 <- PacBioCmpH5(system.file("h5_files",  "aligned_reads.cmp.h5",
  package = "pbh5"))
  values <- getQualityValue(cmpH5)
  class(values)
  length(values)
  length(values[[1]])
  head(values[[1]])