To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("tilingArray")

In most cases, you don't need to download the package archive at all.

tilingArray

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see tilingArray.

Transcript mapping with high-density oligonucleotide tiling arrays

Bioconductor version: 3.0

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>

Citation (from within R, enter citation("tilingArray")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("tilingArray")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("tilingArray")

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, Software, Visualization
Version	1.44.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 11 years)
License	Artistic-2.0
Depends	R (>= 2.11.0), Biobase, methods, pixmap
Imports	strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me	davidTiling
Imports Me	ADaCGH2, snapCGH
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	tilingArray_1.44.0.tar.gz
Windows Binary	tilingArray_1.44.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	tilingArray_1.44.0.tgz
Mac OS X 10.9 (Mavericks)	tilingArray_1.44.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/tilingArray/tree/release-3.0
Package Short Url	http://bioconductor.org/packages/tilingArray/
Package Downloads Report	Download Stats