R453Plus1Toolbox (version 1.22.0)

getAlignedReads: Import reads from an Amplicon Variant Analyzer project

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.

Value

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

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.

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)