tilingArray-package {tilingArray} | R Documentation

## tilingArray package overview

### Description

tilingArray package overview

### Details

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).

### Author(s)

W. Huber <huber@ebi.ac.uk>

[Package tilingArray version 1.64.0 Index]