MPAgenomics: Multi-Patient Analysis of Genomic Markers

Preprocess and analysis of genomic data. MPAgenomics provides wrappers from commonly used packages to streamline their repeated manipulation, offering an easy-to-use pipeline. The segmentation of successive multiple profiles is performed with an automatic choice of parameters involved in the wrapped packages. Considering multiple profiles in the same time, MPAgenomics wraps efficient penalized regression methods to select relevant markers associated with a given outcome.

AuthorQuentin Grimonprez with contributions from Guillemette Marot and Samuel Blanck. Some functions use code created by Sjoerd Vosse, Mark van de Wiel, Pierre Neuvial, Henrik Bengtsson.
Date of publication2015-09-09 15:03:13
MaintainerSamuel Blanck <samuel.blanck@inria.fr>
LicenseGPL(>=2)
Version1.1.4

View on R-Forge

Functions

addChipType Man page
addData Man page
callingObject Man page
callingProcess Man page
CNAobjectToCGHcallObject Man page
cnSegCallingProcess Man page
createArchitecture Man page
createEmptyArchitecture Man page
filterSeg Man page
findPlateau Man page
getCopyNumberSignal Man page
getFracBSignal Man page
getGenotypeCalls Man page
getListOfFiles Man page
getSymFracBSignal Man page
HDlarsbivariate Man page
markerSelection Man page
MPAgenomics Man page
MPAgenomics-package Man page
MPAgenomics-package, Man page
segFracBSignal Man page
segmentation Man page
segmentationAroma Man page
segmentationObject Man page
SignalNormalization Man page
signalPreProcess Man page
symmetrizeFracB Man page
variableSelection Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/MPAgenomics-package.R R/SNPselection.R R/aromafunctions.R R/bivariateSignal.R R/cghcall.R R/cghcall_preprocess.R R/cghcall_private.R R/cghseg.R R/createAromaArchitecture.R R/expandcghcall.R R/findPlateau.R R/genotypeCalls.R R/getCNSignal.R R/getFracBSignal.R R/getGenotypeCalls.R R/getSymFracBsignal.R R/pelt.R R/segCalling.R R/segFracB.R R/signalPreprocess.R R/tumorboost.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/MPAgenomics.R
inst/doc/MPAgenomics.Rnw
inst/doc/MPAgenomics.pdf
man
man/CNAobjectToCGHcallObject.Rd man/HDlarsbivariate.Rd man/MPAgenomics-package.Rd man/SignalNormalization.Rd man/addChipType.Rd man/addData.Rd man/callingObject.Rd man/callingProcess.Rd man/cnSegCallingProcess.Rd man/createArchitecture.Rd man/createEmptyArchitecture.Rd man/filterSeg.Rd man/findPlateau.Rd man/getCopyNumberSignal.Rd man/getFracBSignal.Rd man/getGenotypeCalls.Rd man/getListOfFiles.Rd man/getSymFracBSignal.Rd man/markerSelection.Rd man/segFracBSignal.Rd man/segmentation.Rd man/segmentationAroma.Rd man/segmentationObject.Rd man/signalPreProcess.Rd man/symmetrizeFracB.Rd man/variableSelection.Rd
vignettes
vignettes/MPAgenomics.Rnw
vignettes/MPAgenomics.bib
vignettes/fig
vignettes/fig/callsoutput.png
vignettes/fig/callsoutput2.png
vignettes/fig/chipFiles2.png
vignettes/fig/classifplateau3.png
vignettes/fig/cvcourbe.png
vignettes/fig/dataFiles.png
vignettes/fig/dataFilesSingle2.png
vignettes/fig/dataResponse.png
vignettes/fig/decdata1.png
vignettes/fig/falsesel.png
vignettes/fig/fracB.png
vignettes/fig/freqdata1.png
vignettes/fig/matrixlabel.png
vignettes/fig/normalTumorArray.png
vignettes/fig/normalTumorArrayExample.png
vignettes/fig/normalTumorArrayExample2.png
vignettes/fig/outbedpelt.png
vignettes/fig/outpelt2.png
vignettes/fig/plateau.png
vignettes/fig/plot1.png
vignettes/fig/plot2.png
vignettes/fig/plot3.png
vignettes/fig/plot4.png
vignettes/fig/segapresfiltre2.png
vignettes/fig/segdata1.png
vignettes/fig/slopeheuristic.png
vignettes/fig/snpselectres.png
vignettes/fig/symFracB.png
vignettes/fig/truesel.png

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