\HeaderA{smlSet-class}{Documentation on
S4 class "smlSet" an eSet-derived container for snpMatrix lists,
allowing efficient combination of SNP chip genotyping with microarray
expression data, and allied classes}{smlSet.Rdash.class}
\aliasA{combine,smlSet,smlSet-method}{smlSet-class}{combine,smlSet,smlSet.Rdash.method}
\aliasA{exprs,smlSet-method}{smlSet-class}{exprs,smlSet.Rdash.method}
\aliasA{getAlleles}{smlSet-class}{getAlleles}
\aliasA{getAlleles,smlSet,rsid-method}{smlSet-class}{getAlleles,smlSet,rsid.Rdash.method}
\aliasA{show,smlSet-method}{smlSet-class}{show,smlSet.Rdash.method}
\aliasA{smlEnv}{smlSet-class}{smlEnv}
\aliasA{smlEnv,smlSet-method}{smlSet-class}{smlEnv,smlSet.Rdash.method}
\aliasA{smList}{smlSet-class}{smList}
\aliasA{smList,smlSet-method}{smlSet-class}{smList,smlSet.Rdash.method}
\aliasA{smlSet}{smlSet-class}{smlSet}
\aliasA{snpNames}{smlSet-class}{snpNames}
\aliasA{snpNames,smlSet,chrnum-method}{smlSet-class}{snpNames,smlSet,chrnum.Rdash.method}
\aliasA{snpNames,smlSet,missing-method}{smlSet-class}{snpNames,smlSet,missing.Rdash.method}
\aliasA{snps}{smlSet-class}{snps}
\aliasA{snps,smlSet,chrnum-method}{smlSet-class}{snps,smlSet,chrnum.Rdash.method}
\aliasA{[,smlSet,ANY,ANY,ANY-method}{smlSet-class}{[,smlSet,ANY,ANY,ANY.Rdash.method}
\aliasA{[,snp.matrix,ANY,rsid,ANY-method}{smlSet-class}{[,snp.matrix,ANY,rsid,ANY.Rdash.method}
\keyword{classes}{smlSet-class}
\begin{Description}\relax
Documentation on
S4 class "smlSet" an eSet-derived container for snpMatrix lists,
allowing efficient combination of SNP chip genotyping with microarray
expression data, and allied classes
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("smlSet", assayData, phenoData, featureData, experimentData, annotation, ...)}.
These objects respond to interrogation on samples, expression values,
SNP values, and other metadata.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{smlEnv}:] Object of class \code{"environment"} an environment
with single key \code{smList} pointing to a list of
package snpMatrix snp.matrix instances 
\item[\code{organism}:] Object of class \code{"character"} informal,
"Hs" recommended for human 
\item[\code{assayData}:] Object of class \code{"AssayData"} intended
to hold expression data coordinated with the smlEnv data 
\item[\code{phenoData}:] Object of class \code{"AnnotatedDataFrame"} 
standard sample-level data container from eSet design 
\item[\code{featureData}:] Object of class \code{"AnnotatedDataFrame"} 
standard feature-level metadata container, implied usage is for documenting
the expresion data elements 
\item[\code{experimentData}:] Object of class \code{"MIAME"} standard
metadata container from Biobase eSet design 
\item[\code{annotation}:] Object of class \code{"character"} vector
giving the Bioconductor annotation package
(.db type) for decoding expression feature identifiers. 
\item[\code{.\_\_classVersion\_\_}:] Object of class \code{"Versions"} class
version tracking metadata 
}
\end{Section}
\begin{Section}{Extends}
Class \code{\LinkA{eSet}{eSet}}, directly.
Class \code{\LinkA{VersionedBiobase}{VersionedBiobase}}, 
by class "eSet", distance 2.
Class \code{\LinkA{Versioned}{Versioned}}, by class "eSet", 
distance 3.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[smList] \code{signature(x = "smlSet")}: retrieves the
actual list of snp.matrix entities 
\item[smlEnv] \code{signature(x = "smlSet")}: retrieves the
environment holding snp.matrix entities 
\item[exprs] \code{signature(x = "smlSet")}: retrieves the
matrix of expression values 
\item[snps] \code{signature(x = "smlSet", chr = "chrnum")}: retrieves the
raw matrix of genotype values (snp.matrix instance from
snpMatrix package 
\item[\code{combine}:] concatenates expression
data and forms intersection of SNP sets
\item[\code{getAlleles(smlSet, rsid)}:] returns A/B notations for SNP
determined by rsid
}
\end{Section}
\begin{Note}\relax
We have included a \code{[} method for snp.matrix instances
that accepts an rsid instance as a column selector.
\end{Note}
\begin{Author}\relax
VJ Carey \textless{}stvjc@channing.harvard.edu\textgreater{}
\end{Author}
\begin{SeeAlso}\relax
GGtools package makes extensive use of these classes and methods.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("smlSet")
\end{ExampleCode}
\end{Examples}

