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tilingArray

This is the development version of tilingArray; for the stable release version, see tilingArray.

Transcript mapping with high-density oligonucleotide tiling arrays


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
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
Segmentation demo PDF
Supplement. Calculation of the cost matrix PDF
Reference Manual PDF

Details

biocViews Microarray, OneChannel, Preprocessing, Software, Visualization
Version 1.81.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License Artistic-2.0
Depends R (>= 2.11.0), Biobase, methods, pixmap
Imports strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
System Requirements
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Depends On Me davidTiling
Imports Me ADaCGH2
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Package Archives

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

Source Package tilingArray_1.81.0.tar.gz
Windows Binary tilingArray_1.81.0.zip
macOS Binary (x86_64) tilingArray_1.81.0.tgz
macOS Binary (arm64) tilingArray_1.81.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tilingArray
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tilingArray
Bioc Package Browser https://code.bioconductor.org/browse/tilingArray/
Package Short Url https://bioconductor.org/packages/tilingArray/
Package Downloads Report Download Stats