rMAT

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see rMAT.

R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.


Bioconductor version: 3.9

This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and Bioconductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments. Note: users should have GSL and GenomeGraphs installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch!

Author: Charles Cheung and Arnaud Droit and Raphael Gottardo

Maintainer: Arnaud Droit <arnaud.droit at crchuq.ulaval.ca> and Raphael Gottardo <rgottard at fhcrc.org>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("rMAT")

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("rMAT")
The rMAT users guide PDF R Script
Reference Manual PDF

Details

biocViews Microarray, Preprocessing, Software
Version 3.33.0
In Bioconductor since BioC 2.4 (R-2.9) (15 years)
License Artistic-2.0
Depends R (>= 2.9.0), BiocGenerics(>= 0.1.3), IRanges(>= 1.13.10), Biobase(>= 2.15.1), affxparser
Imports stats, methods, BiocGenerics, IRanges, Biobase, affxparser, stats4
System Requirements GSL (GNU Scientific Library)
URL http://www.rglab.org
See More
Suggests GenomeGraphs, rtracklayer
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Package Archives

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

Source Package rMAT_3.33.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) rMAT_3.33.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rMAT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rMAT
Bioc Package Browser https://code.bioconductor.org/browse/rMAT/
Package Short Url https://bioconductor.org/packages/rMAT/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive