Biostrings (version 2.40.2)

QualityScaledXStringSet-class: 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.

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.

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.

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