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 (3.21)

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Microarray, OneChannel, Preprocessing, Software, Visualization
Version	1.85.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 19.5 years)
License	Artistic-2.0
Depends	R (>= 2.11.0), Biobase, methods, pixmap
Imports	strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
System Requirements
URL

Suggests
Linking To
Enhances
Depends On Me	davidTiling
Imports Me	ADaCGH2
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	tilingArray_1.85.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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