getUnrolledTemplateSpan: Compute the Unrolled Template Span

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

Description

'getUnrolledTemplateSpan' commputes the unrolled template span.

Usage

  getUnrolledTemplateSpan(cmpH5, idx = 1:nrow(cmpH5), unique = TRUE)

Arguments

cmpH5	An object of class PacBioCmpH5.
idx	The indices of the alignments to retrieve.
unique	Boolean statement whether the unrolled template span is unique.

Details

The getUnrolledTemplateSpan is based on the getMoleculeIndex function which returns a vector of length(idx) of type factor designating the molecule's ID. the vector is ordered as idx, therefore the default behavior of idx = 1:nrow(cmpH5) means that the vector is as the cmpH5 object – this is only distinct from other functions in that there are repeats in the vector, hence the unique = TRUE argument of getUnrolledTemplateSpan.

Value

'getUnrolledTemplateSpan' returns an array with molecule index and the unrolled span length.

Examples

  gc()
  require(pbh5)
  cmpH5 <- PacBioCmpH5(system.file("h5_files",  "aligned_reads.cmp.h5",
  package = "pbh5"))
  mi <- getMoleculeIndex(cmpH5)
  head(mi)
  uts <- getUnrolledTemplateSpan(cmpH5)
  head(uts)
  ylim = c(0, 0.0015)
  xlim = c(-1000, 5000)
  plot(density(uts), xlim = xlim, ylim = ylim, xlab = '', main = '', col
  = 'red', lwd = 2)
  par(new = TRUE)
  plot(density(getTemplateSpan(cmpH5)), xlim = xlim, ylim = ylim, xlab =
  '', main = '', lwd = 2)
  legend('topright',legend = c('unrolledTemplateSpan', 'templateSpan'),
  fill = c('red', 'black'))

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