tilingArray-package: tilingArray package overview
In tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays

tilingArray package overview

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:

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