restrictCmpH5: Limit a cmpH5 to a subset of the reads.

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

Description

Construct a new cmpH5 object representing the subset of reads specified in mask.

Usage

  restrictCmpH5(cmpH5, mask = rep(TRUE, nrow(cmpH5)))

Arguments

cmpH5	An object of type PacBioCmpH5
mask	A vector or booleans.

Details

Some of the the finer details of the cmpH5 object are not changed. For instance, the sorting facility in cmpH5 supports an index for performance, by filtering out certain reads the accuracy of these indexes is off, which will make certain operations slower.

Value

A new cmpH5 file.

Examples

  cmpH5 <- PacBioCmpH5(system.file("h5_files",  "aligned_reads.cmp.h5", package = "pbh5"))
  nrow(restrictCmpH5(cmpH5, getReadLength(cmpH5) < 500))

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