getIPD: Compute the IPD
In PacificBiosciences/R-pbh5: Interface to Pacific Biosciences HDF5 Files

Description Usage Arguments Details Value See Also Examples

'getIPD' computes the inter-pulse duration for each base.

1	getIPD(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.

Inter-pulse distances are given in seconds.

A list of vectors of inter-pulse distances.

PacBioCmpH5-class

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