QualityScore {ShortRead} | R Documentation

## Construct objects indicating read or alignment quality

### Description

Use these functions to construct quality indicators for reads or alignments. See `QualityScore` for details of object content and methods available for manipulating them.

### Usage

    NumericQuality(quality = numeric(0))
    IntegerQuality(quality = integer(0))
    MatrixQuality(quality = new("matrix"))
    FastqQuality(quality, ...)
    SFastqQuality(quality, ...)

### Arguments

`quality` | An object used to initialize the data structure. Appropriate objects are indicated in the constructors above for Numeric, Integer, and Matrix qualities. For `FastqQuality` and `SFastqQuality`, methods are defined for `BStringSet`, `character`, and `missing`.
`...` | Additional arguments, currently unused.

### Value

Constructors return objects of the corresponding class derived from `QualityScore`.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`QualityScore`, `readFastq`, `readAligned`

### Examples

    nq <- NumericQuality(rnorm(20))
    nq
    quality(nq)
    quality(nq[10:1])

[Package ShortRead version 1.45.4 Index]