XStringQuality-class       package:Biostrings       R Documentation

PhredQuality and SolexaQuality objects

Description:

     Objects for storing string quality measures.

Usage:

       ## Constructors:
       PhredQuality(x)
       SolexaQuality(x)

Arguments:

       x: Either a character vector, BString, BStringSet, integer
          vector, or number vector of error probabilities. 

Details:

     'PhredQuality' objects store characters that are interpreted as [0
     - 99] quality measures by subtracting 33 from their ASCII decimal
     representation (e.g. ! = 0, " = 1, # = 2, ...).

     'SolexaQuality' objects store characters are interpreted as [-5 -
     99] quality measures by subtracting 64 from their ASCII decimal
     representation (e.g. ; = -5, < = -4, = = -3, ...).

Author(s):

     P. Aboyoun

See Also:

     'pairwiseAlignment', PairwiseAlignedXStringSet-class,
     DNAString-class, BStringSet-class

Examples:

       PhredQuality(0:40)
       SolexaQuality(0:40)

       PhredQuality(seq(1e-4,0.5,length=10))
       SolexaQuality(seq(1e-4,0.5,length=10))

