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

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!

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rMAT")
AuthorCharles Cheung and Arnaud Droit and Raphael Gottardo
Bioconductor views Microarray Preprocessing
Date of publicationNone
MaintainerArnaud Droit <arnaud.droit@crchuq.ulaval.ca> and Raphael Gottardo <rgottard@fhcrc.org>
LicenseArtistic-2.0
Version3.26.0
http://www.rglab.org

View on Bioconductor

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/BPMAPCelMerger.R R/BPMAPCelParser.R R/MATScore.R R/NormalizeProbes.R R/ReadBPMAPAllSeqHeader.R R/ReadBPMAPHeader.R R/ReadBPMAPSeq.R R/SetClasses.R R/SetMethods.R
aclocal.m4
build
build/vignette.rds
cleanup
configure
configure.ac
inst
inst/doc
inst/doc/rMAT.R
inst/doc/rMAT.Rnw
inst/doc/rMAT.pdf
inst/extdata
inst/extdata/Sc03b_MR_v04_10000.bpmap
inst/extdata/Swr1WTIP_Short.CEL
man
man/BPMAPCelParser.Rd man/MATScore.Rd man/NormalizeProbes.Rd man/ReadBPMAPAllSeqHeader.Rd man/callEnrichedRegions.Rd man/computeMATScore.Rd man/show.Rd man/summary.Rd man/tillingSet.Rd
scripts
scripts/Viewport.R scripts/test.R
src
src/BARFileData.cpp
src/BARFileData.h
src/BARFileWriter.cpp
src/BARFileWriter.h
src/BARReader.cpp
src/BARWriter.cpp
src/BPMAPFileData.cpp
src/BPMAPFileData.h
src/BPMAPfunctions.cpp
src/DeclareAll.c
src/FileIO.cpp
src/FileIO.h
src/FileWriter.cpp
src/FileWriter.h
src/Makevars.in
src/Makevars.win
src/NormalizeProbes.c
src/Rdefines.h
src/TagValuePair.h
src/affy-base-types.h
src/config.h.in
vignettes
vignettes/MyBedFile.bed
vignettes/README
vignettes/rMAT.Rnw

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