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\name{chromLocation-class}
\docType{class}
\alias{chromLocation-class}
\alias{chromLocation}
\alias{dataSource}
\alias{nChrom}
\alias{chromNames}
\alias{chromLocs}
\alias{chromLengths}
\alias{probesToChrom}
\alias{geneSymbols}
\alias{chromInfo}
\alias{organism,chromLocation-method}
\alias{dataSource,chromLocation-method}
\alias{nChrom,chromLocation-method}
\alias{chromNames,chromLocation-method}
\alias{chromLocs,chromLocation-method}
\alias{chromLengths,chromLocation-method}
\alias{probesToChrom,chromLocation-method}
\alias{geneSymbols,chromLocation-method}
\alias{chromInfo,chromLocation-method}
\alias{show,chromLocation-method}
\title{Class chromLocation, a class for describing genes and their
chromosome mappings.}
\description{
This class provides chromosomal information provided by a
Bioconductor metadata package. By creating the object once for a
particular package, it can be used in a variety of locations without
the need to recomputed values repeatedly.
}
\section{Creating Objects}{
\code{ new('chromLocation',}
\code{ organism = ...., # Object of class character}\cr
\code{ dataSource = ...., # Object of class character}\cr
\code{ chromLocs = ...., # Object of class list}\cr
\code{ probesToChrom = ...., # Object of class ANY}\cr
\code{ chromInfo = ...., # Object of class numeric}\cr
\code{ geneSymbols = ...., # Object of class ANY}\cr
\code{ )}}
\section{Slots}{
\describe{
\item{\code{organism}:}{Object of class "character". The organism
that these genes correspond to.}
\item{\code{dataSource}:}{Object of class "character". The source of
the gene data.}
\item{\code{chromLocs}:}{Object of class "list". A list which
provides specific location information for every gene.}
\item{\code{probesToChrom}:}{An object with an environment-like API
which will translate a probe identifier to chromosome it belongs
to.}
\item{\code{chromInfo}:}{A numerical vector representing each
chromosome, where the names are the names of the chromosomes and
the values are their lengths}
\item{\code{geneSymbols}:}{An environment or an object with
environment-like API that maps a probe ID to
the appropriate gene symbol}
}
}
\section{Methods}{
\describe{
\item{chromLengths}{(chromLocation): Gets the lengths of the
chromosome for this organism}
\item{chromLocs}{(chromLocation): Gets the 'chromLocs' attribute.}
\item{chromNames}{(chromLocation): Gets the name of the chromosomes
for this organism}
\item{dataSource}{(chromLocation): Gets the 'dataSource' attribute.}
\item{probesToChrom}{(chromLocation): Gets the 'probesToChrom' attribute.}
\item{nChrom}{(chromLocation): gets the number of chromosomes this
organism has}
\item{organism}{(chromLocation): gets the 'organism' attribute.}
\item{chromInfo}{Gets the 'chromInfo' attribute.}
\item{geneSymbols}{Gets the 'geneSymbols' attribute.}
}
}
\seealso{\code{\link{buildChromLocation}}}
\examples{
library("hgu95av2.db")
z <- buildChromLocation("hgu95av2")
## find the number of chromosomes
nChrom(z)
## Find the names of the chromosomes
chromNames(z)
## get the organism this object refers to
organism(z)
## get the lengths of the chromosomes in this object
chromLengths(z)
}
\keyword{classes}
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