Biostrings (version 2.34.1)

XStringQuality-class: PhredQuality, SolexaQuality and IlluminaQuality objects

Description

Objects for storing string quality measures.

Usage

## Constructors:
PhredQuality(x)
SolexaQuality(x)
IlluminaQuality(x)
## alphabet and encoding
"alphabet"(x)
"encoding"(x)

Arguments

x

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

Alphabet and encoding

In the code snippets below, x is an XStringQuality object.

alphabet(x): Valid letters in this quality score; not all letters are encountered in actual sequencing runs.

encoding(x): Map between letters and their corresponding integer encoding. Use as.integer and as.numeric to coerce objects to their integer and probability representations.

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, ...). Quality measures q encode probabilities as -10 * log10(p).

SolexaQuality objects store characters that are interpreted as [-5 - 99] quality measures by subtracting 64 from their ASCII decimal representation (e.g. ; = -5, < = -4, = = -3, ...). Quality measures q encode probabilities as -10 * (log10(p) - log10(1 - p)).

IlluminaQuality objects store characters that are interpreted as [0 - 99] quality measures by subtracting 64 from their ASCII decimal representation (e.g. @ = 0, A = 1, B = 2, ...). Quality measures q encode probabilities as -10 * log10(p)

See Also

pairwiseAlignment, PairwiseAlignments-class, DNAString-class, BStringSet-class

Examples

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

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

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