\HeaderA{tilingArray-package}{tilingArray package overview}{tilingArray.Rdash.package}
\aliasA{tilingArray}{tilingArray-package}{tilingArray}
\keyword{package}{tilingArray-package}
\begin{Description}\relax
tilingArray package overview
\end{Description}
\begin{Details}\relax
The package provides some functionalities that can be useful for the
analysis of high-density tiling microarray data (such as Affymetrix
genechips) for measuring transcript abundance and architecture.
The main functionalities of the package are:

\Itemize{
\item The segmentation class
for representing partitionings of a linear series of data (such as
microarray intensity readings along a chromosome strand).
\item The function \code{\LinkA{segment}{segment}}
for fitting piecewise constant models using a dynamic programming
algorithm that is both fast and exact,
and \code{\LinkA{confint}{confint}} for
calculating confidence intervals using the
strucchange package.
Please see the vignette \emph{Segmentation demo} in the file
inst/doc/segmentation.pdf (source file inst/scripts/segmentation.Rnw).
\item The function \code{\LinkA{plotAlongChrom}{plotAlongChrom}} for generating pretty
plots of segmentations along with genomic features. Please also see
the vignette \emph{Segmentation demo}.
\item The function \code{\LinkA{normalizeByReference}{normalizeByReference}}
for probe-sequence dependent response adjustment from 
a (set of) reference hybridizations.
Please see the vignette \emph{Assessing signal/noise ratio before and after normalization} in the file
inst/doc/assessNorm.pdf (source file inst/scripts/assessNorm.Rnw).
}
\end{Details}
\begin{Author}\relax
W. Huber <huber@ebi.ac.uk>
\end{Author}

