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\name{XStringQuality-class}
\docType{class}
% Classes:
\alias{class:XStringQuality}
\alias{XStringQuality-class}
\alias{XStringQuality}
\alias{class:PhredQuality}
\alias{PhredQuality-class}
\alias{PhredQuality}
\alias{class:SolexaQuality}
\alias{SolexaQuality-class}
\alias{SolexaQuality}
\alias{class:IlluminaQuality}
\alias{IlluminaQuality-class}
\alias{IlluminaQuality}
% Coercion:
\alias{coerce,character,PhredQuality-method}
\alias{coerce,BString,PhredQuality-method}
\alias{coerce,BStringSet,PhredQuality-method}
\alias{coerce,integer,PhredQuality-method}
\alias{coerce,numeric,PhredQuality-method}
\alias{coerce,IntegerList,PhredQuality-method}
\alias{coerce,NumericList,PhredQuality-method}
\alias{coerce,character,SolexaQuality-method}
\alias{coerce,BString,SolexaQuality-method}
\alias{coerce,BStringSet,SolexaQuality-method}
\alias{coerce,integer,SolexaQuality-method}
\alias{coerce,numeric,SolexaQuality-method}
\alias{coerce,IntegerList,SolexaQuality-method}
\alias{coerce,NumericList,SolexaQuality-method}
\alias{coerce,character,IlluminaQuality-method}
\alias{coerce,BString,IlluminaQuality-method}
\alias{coerce,BStringSet,IlluminaQuality-method}
\alias{coerce,integer,IlluminaQuality-method}
\alias{coerce,numeric,IlluminaQuality-method}
\alias{coerce,IntegerList,IlluminaQuality-method}
\alias{coerce,NumericList,IlluminaQuality-method}
\alias{as.vector,XStringQuality-method}
\alias{coerce,XStringQuality,IntegerList-method}
\alias{coerce,XStringQuality,NumericList-method}
\alias{as.matrix,XStringQuality-method}
\alias{coerce,XStringQuality,matrix-method}
%% alphabet & encoding
\alias{alphabet,XStringQuality-method}
\alias{encoding}
\alias{encoding,XStringQuality-method}
\title{PhredQuality, SolexaQuality and IlluminaQuality objects}
\description{
Objects for storing string quality measures.
}
\usage{
## Constructors:
PhredQuality(x)
SolexaQuality(x)
IlluminaQuality(x)
## alphabet and encoding
\S4method{alphabet}{XStringQuality}(x)
\S4method{encoding}{XStringQuality}(x)
}
\arguments{
\item{x}{
Either a character vector, \link{BString}, \link{BStringSet},
integer vector, or number vector of error probabilities.
}
}
\details{
\code{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 \code{-10 * log10(p)}.
\code{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 \code{-10 * (log10(p) - log10(1 - p))}.
\code{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 \code{-10 * log10(p)}
}
\section{Alphabet and encoding}{
In the code snippets below, \code{x} is an XStringQuality object.
\describe{
\item{}{
\code{alphabet(x)}: Valid letters in this quality score; not all
letters are encountered in actual sequencing runs.
}
\item{}{
\code{encoding(x)}: Map between letters and their corresponding
integer encoding. Use \code{as.integer} and \code{as.numeric} to
coerce objects to their integer and probability representations.
}
}
}
\author{P. Aboyoun}
\seealso{
\code{\link{pairwiseAlignment}},
\link{PairwiseAlignments-class},
\link{DNAString-class},
\link{BStringSet-class}
}
\examples{
PhredQuality(0:40)
SolexaQuality(0:40)
IlluminaQuality(0:40)
pq <- PhredQuality(c("*+,-./", "0123456789:;"))
qs <- as(pq, "IntegerList") # quality scores
qs
as(qs, "PhredQuality")
p <- as(pq, "NumericList") # probabilities
as(p, "PhredQuality")
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(x, "IntegerList") # quality scores
as(x, "NumericList") # probabilities
as.matrix(x) # quality scores
}
\keyword{methods}
\keyword{classes}
|
