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\name{Cdf-class}
\docType{class}
\alias{Cdf-class}
\alias{atom}
\alias{atom<-}
\alias{name.levels}
\alias{name.levels<-}
\alias{pbase}
\alias{pbase<-}
\alias{pbase.levels}
\alias{pbase.levels<-}
\alias{tbase}
\alias{tbase<-}
\alias{tbase.levels}
\alias{tbase.levels<-}
\alias{atom,Cdf-method}
\alias{atom<-,Cdf-method}
\alias{name.levels,Cdf-method}
\alias{name.levels<-,Cdf-method}
\alias{pbase,Cdf-method}
\alias{pbase<-,Cdf-method}
\alias{pbase.levels,Cdf-method}
\alias{pbase.levels<-,Cdf-method}
\alias{tbase,Cdf-method}
\alias{tbase<-,Cdf-method}
\alias{tbase.levels,Cdf-method}
\alias{tbase.levels<-,Cdf-method}
\alias{show,Cdf-method}
\title{Class Cdf}
\description{A class describing the content a Chip Description File.}
\section{Creating Objects}{
\code{ new('Cdf',}\cr
\code{ cdfName = ...., # Object of class character}\cr
\code{ name = ...., # Object of class matrix}\cr
\code{ name.levels = ...., # Object of class character}\cr
\code{ pbase = ...., # Object of class matrix}\cr
\code{ pbase.levels = ...., # Object of class character}\cr
\code{ tbase = ...., # Object of class matrix}\cr
\code{ tbase.levels = ...., # Object of class character}\cr
\code{ atom = ...., # Object of class matrix}\cr
\code{ )}}
\section{Slots}{
\describe{
\item{\code{cdfName}:}{the CDF name tag. Used to link with the right
CEL files}
\item{\code{name}:}{Object of class "matrix" of 'factors' for the gene names corresponding to the probes.}
\item{\code{name.levels}:}{Object of class "character" containing
the levels corresponding to \code{name}.}
\item{\code{pbase}:}{Object of class "matrix" of pbase levels.}
\item{\code{pbase.levels}:}{Object of class "character" containing
the levels corresponding to \code{pbase}. }
\item{\code{tbase}:}{Object of class "matrix" of tbase levels.}
\item{\code{tbase.levels}:}{Object of class "character" containing
the levels corresponding to \code{tbase}. }
\item{\code{atom}:}{Object of class "matrix" of atom or probe numbers.}
}
}
\details{
The class \code{Cdf} was designed to store the content of Affymetrix's
Chip Definition Files (CDF). This early class is no longer widely used
in the package affy. Environments (called \code{cdfenvs}) are
preferred to have an efficient mapping between probe set identifiers
and indexes (needed to access/subset particular probe intensities).
Unless one needs to access every information contained in a
CDF file, the \code{cdfenvs} will be preferred.
The following comments are only relevant to someone with interest in
what is in a CDF file.
The name associated
to each probe is not unique, it corresponds to the gene name. It is
very common to have a name repeated 40 times (20 perfect matches and 20
mismatches). Probes can be grouped by pairs: a perfect
match (PM) probe has its mismatch (MM) counterpart. The two probes in a
pair differ by one base (usually located in the middle of the
sequence). The information relative to this particular base are stored
in \code{pbase} and \code{tbase}. At a given position (x,y), having
pbase[x,y] == tbase[x,y] means having a MM while having pbase[x,y] !=
tbase[x,y] means having a perfect mismatch if and only if one of the
bases is A while the other is TRUE, or one is G and the other is C. The
function
\code{\link{pmormm}} returns \code{TRUE} for PMs and \code{FALSE} for
MMs.
To know more about the file structure of a CDF file, one has to refer
to the parsing code (mostly in C).
}
\seealso{
\code{\link{read.cdffile}},
\code{\link{make.cdf.env}},
\code{\link{make.cdf.package}}
}
\author{L. Gautier <laurent@cbs.dtu.dk>}
\section{Methods}{
\describe{
\item{atom}{(Cdf): An accesor function for the
\code{ato,} slot. }
\item{atom<-}{(Cdf): A replacement function for
\code{atom} slot. }
\item{name.levels}{(Cdf): An accesor function for the
\code{name.levels} slot. }
\item{name.levels<-}{(Cdf): A replacement function for
\code{name.levels} slot. }
\item{pbase}{(Cdf): An accesor function for the
\code{pbase} slot. }
\item{pbase<-}{(Cdf): A replacement function for
\code{pbase} slot. }
\item{pbase.levels}{(Cdf): An accesor function for the
\code{pbase.levels} slot. }
\item{pbase.levels<-}{(Cdf): A replacement function for
\code{pbase.levels} slot. }
\item{show}{(Cdf): renders information about the \code{Cdf}
object in a concise way on stdout. }
\item{tbase}{(Cdf): An accesor function for the
\code{tbase} slot. }
\item{tbase<-}{(Cdf): A replacement function for
\code{tbase} slot. }
\item{tbase.levels}{(Cdf): An accesor function for the
\code{tbase.levels} slot. }
\item{tbase.levels<-}{(Cdf): A replacement function for
\code{tbase.levels} slot. }
}
}
\keyword{methods}
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