tilingArray

Transcript mapping with high-density oligonucleotide tiling arrays

Bioconductor version: Development (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

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("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

Reference Manual

Details

biocViews	Microarray, OneChannel, Preprocessing, Visualization
Depends	R, Biobase, methods, pixmap
Imports	strucchange, affy, vsn, genefilter, RColorBrewer, grid
Suggests
System Requirements
License	Artistic-2.0
URL
Depends On Me	ADaCGH2
Imports Me	snapCGH
Suggests Me
Version	1.29.0

Package Downloads

Package Source	tilingArray_1.29.0.tar.gz
Windows Binary	tilingArray_1.29.0.zip (32-bit only)
MacOS 10.5 (Leopard) binary	tilingArray_1.29.0.tgz
Package Downloads Report	Download Stats