tilingArray

Transcript mapping with high-density oligonucleotide tiling arrays

Bioconductor version: Release (2.7)

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 1.28.0

Package Downloads

Package Source tilingArray_1.28.0.tar.gz
Windows Binary tilingArray_1.28.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary tilingArray_1.28.0.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center