getAlignedReads {R453Plus1Toolbox} | R Documentation

## 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.

### 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)

[Package R453Plus1Toolbox version 1.28.1 Index]