\HeaderA{upstreamSeqs-class}{Class "upstreamSeqs"}{upstreamSeqs.Rdash.class}
\aliasA{getUpstream}{upstreamSeqs-class}{getUpstream}
\aliasA{keys}{upstreamSeqs-class}{keys}
\aliasA{keys,upstreamSeqs-method}{upstreamSeqs-class}{keys,upstreamSeqs.Rdash.method}
\aliasA{Nmers}{upstreamSeqs-class}{Nmers}
\aliasA{Nmers,numeric,character,upstreamSeqs-method}{upstreamSeqs-class}{Nmers,numeric,character,upstreamSeqs.Rdash.method}
\aliasA{organism}{upstreamSeqs-class}{organism}
\aliasA{organism,upstreamSeqs-method}{upstreamSeqs-class}{organism,upstreamSeqs.Rdash.method}
\aliasA{seqs}{upstreamSeqs-class}{seqs}
\aliasA{seqs,upstreamSeqs-method}{upstreamSeqs-class}{seqs,upstreamSeqs.Rdash.method}
\aliasA{show,upstreamSeqs-method}{upstreamSeqs-class}{show,upstreamSeqs.Rdash.method}
\keyword{classes}{upstreamSeqs-class}
\begin{Description}\relax
container for a collection of upstream sequences
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("upstreamSeqs", ...)}.
Environments are used to store collections of DNAstrings.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{seqs}:] Object of class \code{"environment"} ~~ 
\item[\code{chrom}:] Object of class \code{"environment"} ~~ 
\item[\code{revComp}:] Object of class \code{"environment"} ~~ 
\item[\code{type}:] Object of class \code{"environment"} ~~ 
\item[\code{organism}:] Object of class \code{"character"} ~~ 
\item[\code{provenance}:] Object of class \code{"ANY"} ~~ 
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[Nmers] \code{signature(n = "numeric", orf = "character", usobj = "upstreamSeqs")}: obtain
all subsequences of length n as view elements of a DNA string 
\item[keys] \code{signature(x = "upstreamSeqs")}: ... 
\item[organism] \code{signature(x = "upstreamSeqs")}: ... 
\item[seqs] \code{signature(x = "upstreamSeqs")}: ... 
\item[show] \code{signature(object = "upstreamSeqs")}: ... 
}
\end{Section}
\begin{Author}\relax
~~who you are~~
\end{Author}
\begin{Examples}
\begin{ExampleCode}
showClass("upstreamSeqs")
data(sceUpstr)
sceUpstr
keys(sceUpstr)[1:5]
\end{ExampleCode}
\end{Examples}

