QualityScaledXStringSet-class   package: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

