getBasecalls: Get Basecall-level Data From pls.h5 or bas.h5 Files.

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

Description

These functions take an object of class bas.h5 or pls.h5 and return vectors for each ZMW represented by holeNumbers (all ZMWs) if no holeNumbers argument is given. Frequently, not all of these values are present in a bas.h5 or pls.h5 file and therefore users should either check or catch and error.

Usage

   getBasecalls(basH5, holeNumbers = getHoleNumbers(basH5), ...)

Arguments

basH5	An object of class PacBioBasH5.
holeNumbers	which ZMWs to grab.
...	Extra arguments to getBaseDataset

Value

A list of character vectors (or whatever object the function convert returns).

Examples

basFiles <- list.files(system.file("h5_files", package = "pbh5"),
                       pattern = "bas", full.names = TRUE)
cmpFiles <- list.files(system.file("h5_files", package = "pbh5"),
                       pattern = "cmp", full.names = TRUE)

## instantiate the bas.h5 files and name them to work with some of the
## paired cmp.h5 bas.h5 functionality.
basH5s <- lapply(basFiles, PacBioBasH5)
names(basH5s) <- sapply(basH5s, getMovieName)

## returns the basecalls for holenumbers 1 and 2.
getBasecalls(basH5s[[1]], holeNumbers = 1:2)

## returns the most probable deleted base. 
getDeletionTag(basH5s[[1]], holeNumbers = 1:2)

## gets the index into the pulse calls.
getPulseIndex(basH5s[[1]], holeNumbers = 1:2)

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