\HeaderA{snpMeta-class}{Class "snpMeta" -- HapMap (or Wellcome INBREDS) -based metadata structures for SNPs}{snpMeta.Rdash.class}
\aliasA{chr20meta}{snpMeta-class}{chr20meta}
\aliasA{chromosome}{snpMeta-class}{chromosome}
\aliasA{chromosome,snpMeta-method}{snpMeta-class}{chromosome,snpMeta.Rdash.method}
\aliasA{coerce,snpMeta,data.frame-method}{snpMeta-class}{coerce,snpMeta,data.frame.Rdash.method}
\aliasA{dim,snpMeta-method}{snpMeta-class}{dim,snpMeta.Rdash.method}
\aliasA{nrow,snpMeta-method}{snpMeta-class}{nrow,snpMeta.Rdash.method}
\aliasA{pos}{snpMeta-class}{pos}
\aliasA{pos,snpMeta-method}{snpMeta-class}{pos,snpMeta.Rdash.method}
\aliasA{show,snpMeta-method}{snpMeta-class}{show,snpMeta.Rdash.method}
\aliasA{snpMetaWhole}{snpMeta-class}{snpMetaWhole}
\aliasA{snpMetaWhole-class}{snpMeta-class}{snpMetaWhole.Rdash.class}
\aliasA{wrapSNPmetaWh}{snpMeta-class}{wrapSNPmetaWh}
\aliasA{[,snpMeta,ANY,ANY-method}{snpMeta-class}{[,snpMeta,ANY,ANY.Rdash.method}
\aliasA{[,snpMeta-method}{snpMeta-class}{[,snpMeta.Rdash.method}
\keyword{classes}{snpMeta-class}
\begin{Description}\relax
HapMap (or Wellcome INBREDS) -based metadata structures for SNPs
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("snpMeta", ...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{meta}:] Object of class \code{"environment"} holds the table in
the \code{meta} element,
in the form of a \code{data.frame}, with rownames giving the SNP ids,
and columns \code{pos}, \code{strand}
\item[\code{chromosome}:] Object of class \code{"character"} string
identifying chromosome on which SNPs are documented 
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[[] \code{signature(x = "snpMeta")}: select subset using rs number
\item[chromosome] \code{signature(x = "snpMeta")}: obtain chromosome name 
\item[pos] \code{signature(x = "snpMeta")}: obtain named vector of positions 
\item[coerce] \code{signature(from = "snpMeta", to = "data.frame")}: return
data.frame with all metadata 
\item[dim] \code{signature(x = "snpMeta")}: give dimensions 
\item[nrow] \code{signature(x = "snpMeta")}: tell number of entries 
\item[show] \code{signature(object = "snpMeta")}: give abbreviated report of contents
with exemplar records
}
\end{Section}
\begin{Author}\relax
VJ Carey <stvjc@channing.harvard.edu>
\end{Author}
\begin{References}\relax
\url{www.hapmap.org} , \url{www.well.ox.ac.uk/mouse/INBREDS}
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(chr20meta)
chr20meta["rs6060535",]
\end{ExampleCode}
\end{Examples}

