tilingArray

DOI: 10.18129/B9.bioc.tilingArray    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see tilingArray.

Transcript mapping with high-density oligonucleotide tiling arrays

Bioconductor version: 3.8

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 <zxu at embl.de>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("tilingArray")

For older versions of R, please refer to the appropriate Bioconductor release.

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		Normalisation with the normalizeByReference function in the tilingArray package
PDF		Segmentation demo
PDF		Supplement. Calculation of the cost matrix
PDF		Reference Manual

Details

biocViews	Microarray, OneChannel, Preprocessing, Software, Visualization
Version	1.60.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 14 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
Links To Me
Build Report

Package Archives

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

Source Package	tilingArray_1.60.0.tar.gz
Windows Binary	tilingArray_1.60.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	tilingArray_1.60.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tilingArray
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tilingArray
Package Short Url	http://bioconductor.org/packages/tilingArray/
Package Downloads Report	Download Stats