getLocalPolymerizationRate: Compute the local Polymerization Rate

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

Description

'getLocalPolymerizationRate' computes the local polymerization rate within each alignment by dividing each alignment into 10 sections.

Usage

getLocalPolymerizationRate(cmpH5, idx = seq.int(1, nrow(cmpH5)),
                           binFunction = function(aln) {
                                           cut(seq.int(1, nrow(aln)), 10)
})

Arguments

cmpH5	An object of class PacBioCmpH5.
idx	The indices of the alignments to return.
binFunction	A function which partitions each alignment into bins. The default option is 10 bins per alignment.

Value

'getLocalPolymerizationRate' returns a list of arrays with start and end times as well as corresponding local polymerization rates within those time-blocks.

Examples

  require(pbh5)
  gc()
  cmpH5 <- PacBioCmpH5(system.file("h5_files",  "aligned_reads.cmp.h5", package = "pbh5"))
  ## Not run: 
   localRate <- getLocalPolymerizationRate(cmpH5, idx = 1:10)
   boxplot(localRate, ylab = "Local Polymerization Rate", xlab = "IndexNumbers")
  
## End(Not run)

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