getAlignedReads: Import reads from an Amplicon Variant Analyzer project

In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

Description

For a given AVASet, this function imports all aligned reads belonging to all (or some selected) amplicons of all samples.

Usage

getAlignedReads(object, amplicons, dir)

Arguments

object	An instance of the link{AVASet-class}.
amplicons	An (optional) character vector of amplicon names as mentioned in the amplicon feature data (see fDataAmp).
dir	Usually, the method tries to retrieve the path to the AVA project from the given link{AVASet} object. However, if it fails to find the directory, dir can be used to set the root directory of the AVA project.

Details

This function reports all reads for all samples together. If you want to get the reads for some samples individually, try subsetting your AVASet as in the examples below.

Value

One DNAStringSet that contains all aligned reads for all samples (eventually restricted to some given amplicons).

Author(s)

Christoph Bartenhagen

See Also

AVASet-class, fDataAmp

Examples

# load an AVA dataset containing 6 samples, 4 amplicons and 259 variants
data(avaSetExample)

# import all reads for amplicon "TET2_E11.04" of the first sample
avaProjectDir = system.file("extdata", "AVASet", package = "R453Plus1Toolbox")
alnReads = getAlignedReads(avaSetExample[, 1], dir=avaProjectDir, amplicons="TET2_E11.04")
show(alnReads)

R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.