rMAT

DOI: 10.18129/B9.bioc.rMAT    

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

Bioconductor version: Release (3.6)

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rMAT")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("rMAT")

 

PDF	R Script	The rMAT users guide
PDF		Reference Manual

Details

biocViews	Microarray, Preprocessing, Software
Version	3.28.0
In Bioconductor since	BioC 2.4 (R-2.9) (9 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
LinkingTo
Suggests	GenomeGraphs, rtracklayer
SystemRequirements	GSL (GNU Scientific Library)
Enhances
URL	http://www.rglab.org
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	rMAT_3.28.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	rMAT_3.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rMAT
Package Short Url	http://bioconductor.org/packages/rMAT/
Package Downloads Report	Download Stats