\HeaderA{hg18track-class}{Class "hg18track" container for hg18 annotation
found in genome browser track files; class "chrnum" extends
numeric for an indexing application on hg18track objects.}{hg18track.Rdash.class}
\aliasA{chrnum}{hg18track-class}{chrnum}
\aliasA{chrnum,hg18track-method}{hg18track-class}{chrnum,hg18track.Rdash.method}
\aliasA{chrnum,numeric-method}{hg18track-class}{chrnum,numeric.Rdash.method}
\aliasA{chrnum-class}{hg18track-class}{chrnum.Rdash.class}
\aliasA{chromStarts}{hg18track-class}{chromStarts}
\aliasA{chromStarts,hg18track-method}{hg18track-class}{chromStarts,hg18track.Rdash.method}
\aliasA{clipTrk}{hg18track-class}{clipTrk}
\aliasA{clipTrk,hg18track,numeric,numeric,ANY-method}{hg18track-class}{clipTrk,hg18track,numeric,numeric,ANY.Rdash.method}
\aliasA{dataVals}{hg18track-class}{dataVals}
\aliasA{dataVals,hg18track-method}{hg18track-class}{dataVals,hg18track.Rdash.method}
\aliasA{demoTrk19}{hg18track-class}{demoTrk19}
\aliasA{getTrkXY}{hg18track-class}{getTrkXY}
\aliasA{getTrkXY,hg18track,character-method}{hg18track-class}{getTrkXY,hg18track,character.Rdash.method}
\aliasA{getTrkXY,hg18track,missing-method}{hg18track-class}{getTrkXY,hg18track,missing.Rdash.method}
\aliasA{initialize,hg18track-method}{hg18track-class}{initialize,hg18track.Rdash.method}
\aliasA{makeHg18track}{hg18track-class}{makeHg18track}
\aliasA{rangeLocs}{hg18track-class}{rangeLocs}
\aliasA{rangeLocs,hg18track-method}{hg18track-class}{rangeLocs,hg18track.Rdash.method}
\aliasA{[,hg18track-method}{hg18track-class}{[,hg18track.Rdash.method}
\keyword{classes}{hg18track-class}
\begin{Description}\relax
container for hg18 annotation
found in genome browser track files
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("hg18track", assayData, featureData, experimentData, annotation, dataVals, ...)}.
These are single-sample eSet instances.

Note that \code{demoTrk19} is a restriction of the \code{rawCD4} structure
to the interval of chromosome 19 that was assayed in the ENCODE project for DnaseI hypersensitivity.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{assayData}:] Object of class \code{"AssayData"} \textasciitilde{}\textasciitilde{} 
\item[\code{phenoData}:] Object of class \code{"AnnotatedDataFrame"} \textasciitilde{}\textasciitilde{} 
\item[\code{featureData}:] Object of class \code{"AnnotatedDataFrame"} \textasciitilde{}\textasciitilde{} 
\item[\code{experimentData}:] Object of class \code{"MIAME"} \textasciitilde{}\textasciitilde{} 
\item[\code{annotation}:] Object of class \code{"character"} \textasciitilde{}\textasciitilde{} 
\item[\code{.\_\_classVersion\_\_}:] Object of class \code{"Versions"} \textasciitilde{}\textasciitilde{} 
}
\end{Section}
\begin{Section}{Extends}
Class \code{"\LinkA{eSet}{eSet.Rdash.class}"}, directly.
Class \code{"\LinkA{VersionedBiobase}{VersionedBiobase.Rdash.class}"}, by class "eSet", distance 2.
Class \code{"\LinkA{Versioned}{Versioned.Rdash.class}"}, by class "eSet", distance 3.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[[] \code{signature(x = "hg18track")}: select using
numeric, logical, or chrnum indices. 
\item[chrnum] \code{signature(object = "hg18track")}: extract
numeric tokens for chromosome number at which data values are
obtained; note that chrnum is also used as name of
a class.
\item[dataVals] \code{signature(object = "hg18track")}: actual
data values 
\item[getTrkXY] \code{signature(object = "hg18track", type = "character")}: obtain a list with components x, y indicating location and
data value respectively; location is within chromosome; default type
is 'midpoint' of locations given as intervals 
\item[getTrkXY] \code{signature(object = "hg18track", type = "missing")}: 
take default midpoint x values corresponding to data values 
\item[rangeLocs] \code{signature(object = "hg18track")}: if measures from
only one chromosome are present , this returns low and high values of chromStart
and chromEnd respectively, otherwise error.
\item[clipTrk] \code{signature(obj = "hg18track",
         low="numeric", hi="numeric", attr="ANY")}: create a restriction
of the track using an interval specification.  by default
the \code{chromStart} featureData component is used for
coordinates to clip; if \code{attr} is non-missing, the
featureData component named by \code{attr} will be used.
\item[initialize] \code{signature(.Object = "hg18track")}: create
a new instance 
}
\end{Section}
\begin{Author}\relax
VJ Carey \textless{}stvjc@channing.harvard.edu\textgreater{}
\end{Author}
\begin{Examples}
\begin{ExampleCode}
showClass("hg18track")
data(rawCD4)
rawCD4
rawCD4.chr1 = rawCD4[ chrnum(1), ]
rangeLocs(rawCD4.chr1)
plot(getTrkXY(rawCD4.chr1), ylab="data value", xlab="interval midpt on chr 1" )
c52 = clipTrk(rawCD4[ chrnum(5), ], 1.30e8, 1.33e8 )
plot(getTrkXY(c52))
\end{ExampleCode}
\end{Examples}

