tilingArray

Transcript mapping with high-density oligonucleotide tiling arrays

Bioconductor version: 2.8

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

Maintainer: Zhenyu Xu <zhenyu at ebi.ac.uk>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("tilingArray")

To cite this package in a publication, start R and enter:

    citation("tilingArray")

Documentation

PDF R Script Introduction to the plotAlongChrom function
PDF R Script Introduction to using the segment function to fit a piecewise constant curve
PDF R Script Normalisation with the normalizeByReference function in the tilingArray package
PDF R Script Segmentation demo
PDF R Script Supplement. Calculation of the cost matrix
PDF   Reference Manual

Details

biocViews Microarray, OneChannel, Preprocessing, Visualization
Depends R (>= 2.11.0), Biobase, methods, pixmap
Imports strucchange, affy, vsn, genefilter, RColorBrewer, grid
Suggests
System Requirements
License Artistic-2.0
URL
Depends On Me ADaCGH2, davidTiling
Imports Me snapCGH
Suggests Me
Version 1.30.0
Since Bioconductor 2.2 (R-2.7)

Package Downloads

Package Source tilingArray_1.30.0.tar.gz
Windows Binary tilingArray_1.30.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary tilingArray_1.30.0.tgz
Package Downloads Report Download Stats

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