getPkmid: Computes the Pkmid Values
In PacificBiosciences/R-pbh5: Interface to Pacific Biosciences HDF5 Files

Description Usage Arguments Details Value Examples

'getPkmid' computes the Pkmid values, a component of Nignal to Noise Ratio (SNR). A vector of Pkmid values is computed for each alignment in the cmph5 file.

1	getPkmid(cmpH5, idx)

`cmpH5`	An object of class `PacBioCmpH5`.
`idx`	The indices of the alignments to retrieve.

Pkmid values are calculated from Pulse Sigma and Baseline Sigma values.

'getPkmid' returns a list of vectors with numeric values.

  ## Not run: 
  require(pbh5)
  cmpH5 <- PacBioCmpH5(system.file("h5_files",  "aligned_reads.cmp.h5",
  package = "pbh5"))
  pkmid <- getPkmid(cmpH5, idx = 1:10)
  boxplot(pkmid,
  main = "Distribution of Pkmid values for the first ten alignments")
 
## End(Not run)