rMAT

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

Bioconductor version: Development (2.8)

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 anf 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 and Raphael Gottardo

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("rMAT")    

Documentation

PDF

R Script

The rMAT users guide

Reference Manual

Details

biocViews	Microarray, Preprocessing
Depends	R, IRanges, Biobase, affxparser
Imports	Biobase, methods, IRanges
Suggests	GenomeGraphs, rtracklayer
System Requirements
License	Artistic-2.0
URL	http://www.rglab.org
Depends On Me
Imports Me
Suggests Me
Version	3.1.1

Package Downloads

Package Source	rMAT_3.1.1.tar.gz
Windows Binary	rMAT_3.1.0.zip (32-bit only)
MacOS 10.5 (Leopard) binary	rMAT_3.1.0.tgz
Package Downloads Report	Download Stats