XStringQuality-class {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))

  x <- SolexaQuality(BStringSet(c(a="@ABC", b="abcd")))
  as.matrix(x)

[Package Biostrings version 2.20.1 Index]