The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.
|Author||Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie|
|Bioconductor views||Microarray OneChannel Preprocessing Visualization|
|Maintainer||Zhenyu Xu <[email protected]>|
|Package repository||View on Bioconductor|
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