rMAT

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

Bioconductor version: 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 <arnaud.droit at ircm.qc.ca> and Raphael Gottardo <raphael.gottardo at ircm.qc.ca>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("rMAT")

Documentation

PDF R Script The rMAT users guide
PDF   Reference Manual

Details

biocViews Microarray, Preprocessing
Depends R(>= 2.9.0), IRanges, Biobase, affxparser
Imports Biobase(>= 2.5.5), methods, IRanges
Suggests GenomeGraphs, rtracklayer
System Requirements
License Artistic-2.0
URL http://www.rglab.org
Depends On Me
Imports Me
Suggests Me
Version 3.2.0
Since Bioconductor 2.4 (R-2.9)

Package Downloads

Package Source rMAT_3.2.0.tar.gz
Windows Binary rMAT_3.2.0.zip (32-bit only)
MacOS 10.5 (Leopard) binary rMAT_3.2.0.tgz
Package Downloads Report Download Stats

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