R: QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects

QualityScaledXStringSet-class {Biostrings} | R Documentation

## QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects

### Description

The QualityScaledBStringSet class is a container for storing a `BStringSet` object with an `XStringQuality` object.

Similarly, the QualityScaledDNAStringSet (or QualityScaledRNAStringSet, or QualityScaledAAStringSet) class is a container for storing a `DNAStringSet` (or `RNAStringSet`, or `AAStringSet`) objects with an `XStringQuality` object.

### Usage

      ## Constructors:
      QualityScaledBStringSet(x, quality)
      QualityScaledDNAStringSet(x, quality)
      QualityScaledRNAStringSet(x, quality)
      QualityScaledAAStringSet(x, quality)

### Arguments

`x` | Either a character vector, or an XString, XStringSet or XStringViews object.
`quality` | An XStringQuality object.

### Details

The `QualityScaledBStringSet`, `QualityScaledDNAStringSet`, `QualityScaledRNAStringSet` and `QualityScaledAAStringSet` functions are constructors that can be used to "naturally" turn `x` into an QualityScaledXStringSet object of the desired base type.

### Accessor methods

The QualityScaledXStringSet class derives from the XStringSet class hence all the accessor methods defined for an XStringSet object can also be used on an QualityScaledXStringSet object. Common methods include (in the code snippets below, `x` is an QualityScaledXStringSet object):

  `length(x)`: The number of sequences in `x`.
  `width(x)`: A vector of non-negative integers containing the number of letters for each element in `x`.
  `nchar(x)`: The same as `width(x)`.
  `names(x)`: `NULL` or a character vector of the same length as `x` containing a short user-provided description or comment for each element in `x`.
  `quality(x)`: The quality of the strings.

### Subsetting and appending

In the code snippets below, `x` and `values` are XStringSet objects, and `i` should be an index specifying the elements to extract.

  `x[i]`: Return a new QualityScaledXStringSet object made of the selected elements.

### Author(s)

P. Aboyoun

### See Also

BStringSet-class, DNAStringSet-class, RNAStringSet-class, AAStringSet-class, XStringQuality-class

### Examples

      x1 <- DNAStringSet(c("TTGA", "CTCN"))
      q1 <- PhredQuality(c("*+,-", "6789"))
      qx1 <- QualityScaledDNAStringSet(x1, q1)
      qx1

[Package Biostrings version 2.16.9 Index]