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

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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
Date of publication
None
Maintainer
Arnaud Droit <arnaud.droit@crchuq.ulaval.ca> and Raphael Gottardo <rgottard@fhcrc.org>
License
Artistic-2.0
Version
3.24.0
URLs

View on Bioconductor

Man pages

BPMAPCelParser
BPMAP and CEL files Reader
callEnrichedRegions
Detection of enriched regions
computeMATScore
Detection of enriched regions
MATScore
Detection of enriched regions
NormalizeProbes
Normalize tiling array data using sequence information
ReadBPMAPAllSeqHeader
Reading All the BPMAP Sequence Header
show
show Method for tiling set object
summary
Summary Method for MAT Object
tillingSet
This object contains an ExpressionSet

Files in this package

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