getPulseWidth: Compute the Pulse Width
In PacificBiosciences/R-pbh5: Interface to Pacific Biosciences HDF5 Files

Description Usage Arguments Details Value Examples

'getPulseWidth' computes the pulsewidth for each base.

1	getPulseWidth(cmpH5, idx, unit = c("seconds", "frames"))

`cmpH5`	An object of class `PacBioCmpH5`.
`idx`	The indices of the alignments to retrieve.
`unit`	Whether you want seconds or frames.

Pulsewidth is computed in seconds.

'getPulseWidth' returns a list of vectors with pulsewidths.

  require(pbh5)
  cmpH5 <- PacBioCmpH5(system.file("h5_files",  "aligned_reads.cmp.h5",
  package = "pbh5"))
  pw <- getPulseWidth(cmpH5)
  logPW <- lapply(pw, function(x) log(x))
  plot(density(logPW[[1]], na.rm = TRUE), main = "Distribution of pulse
  widths from the first alignment")