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 publication2014-11-05 20:25:37
MaintainerSamuel Blanck <samuel.blanck@inria.fr>
LicenseGPL (>= 2)
Version1.1.2

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Files in this package

MPAgenomics
MPAgenomics/inst
MPAgenomics/inst/CITATION
MPAgenomics/inst/doc
MPAgenomics/inst/doc/MPAgenomics.R
MPAgenomics/inst/doc/MPAgenomics.Rnw
MPAgenomics/inst/doc/MPAgenomics.pdf
MPAgenomics/NAMESPACE
MPAgenomics/NEWS
MPAgenomics/R
MPAgenomics/R/cghcall_preprocess.R MPAgenomics/R/findPlateau.R MPAgenomics/R/signalPreprocess.R MPAgenomics/R/getCNSignal.R MPAgenomics/R/getSymFracBsignal.R MPAgenomics/R/bivariateSignal.R MPAgenomics/R/pelt.R MPAgenomics/R/segCalling.R MPAgenomics/R/tumorboost.R MPAgenomics/R/SNPselection.R MPAgenomics/R/MPAgenomics-package.R MPAgenomics/R/segFracB.R MPAgenomics/R/expandcghcall.R MPAgenomics/R/getGenotypeCalls.R MPAgenomics/R/aromafunctions.R MPAgenomics/R/cghseg.R MPAgenomics/R/genotypeCalls.R MPAgenomics/R/cghcall.R MPAgenomics/R/createAromaArchitecture.R MPAgenomics/R/getFracBSignal.R MPAgenomics/R/cghcall_private.R
MPAgenomics/vignettes
MPAgenomics/vignettes/MPAgenomics.Rnw
MPAgenomics/vignettes/fig
MPAgenomics/vignettes/fig/snpselectres.png
MPAgenomics/vignettes/fig/callsoutput.png
MPAgenomics/vignettes/fig/outbedpelt.png
MPAgenomics/vignettes/fig/plot2.png
MPAgenomics/vignettes/fig/segapresfiltre2.png
MPAgenomics/vignettes/fig/decdata1.png
MPAgenomics/vignettes/fig/plateau.png
MPAgenomics/vignettes/fig/freqdata1.png
MPAgenomics/vignettes/fig/dataFilesSingle2.png
MPAgenomics/vignettes/fig/plot3.png
MPAgenomics/vignettes/fig/symFracB.png
MPAgenomics/vignettes/fig/truesel.png
MPAgenomics/vignettes/fig/cvcourbe.png
MPAgenomics/vignettes/fig/dataFiles.png
MPAgenomics/vignettes/fig/outpelt2.png
MPAgenomics/vignettes/fig/normalTumorArrayExample.png
MPAgenomics/vignettes/fig/normalTumorArrayExample2.png
MPAgenomics/vignettes/fig/segdata1.png
MPAgenomics/vignettes/fig/classifplateau3.png
MPAgenomics/vignettes/fig/slopeheuristic.png
MPAgenomics/vignettes/fig/callsoutput2.png
MPAgenomics/vignettes/fig/chipFiles2.png
MPAgenomics/vignettes/fig/plot1.png
MPAgenomics/vignettes/fig/normalTumorArray.png
MPAgenomics/vignettes/fig/dataResponse.png
MPAgenomics/vignettes/fig/plot4.png
MPAgenomics/vignettes/fig/matrixlabel.png
MPAgenomics/vignettes/fig/falsesel.png
MPAgenomics/vignettes/fig/fracB.png
MPAgenomics/vignettes/MPAgenomics.bib
MPAgenomics/MD5
MPAgenomics/build
MPAgenomics/build/vignette.rds
MPAgenomics/DESCRIPTION
MPAgenomics/man
MPAgenomics/man/getSymFracBSignal.Rd MPAgenomics/man/segmentationAroma.Rd MPAgenomics/man/markerSelection.Rd MPAgenomics/man/CNAobjectToCGHcallObject.Rd MPAgenomics/man/createArchitecture.Rd MPAgenomics/man/addChipType.Rd MPAgenomics/man/HDlarsbivariate.Rd MPAgenomics/man/segmentationObject.Rd MPAgenomics/man/segmentation.Rd MPAgenomics/man/getGenotypeCalls.Rd MPAgenomics/man/filterSeg.Rd MPAgenomics/man/callingObject.Rd MPAgenomics/man/segFracBSignal.Rd MPAgenomics/man/callingProcess.Rd MPAgenomics/man/getListOfFiles.Rd MPAgenomics/man/signalPreProcess.Rd MPAgenomics/man/cnSegCallingProcess.Rd MPAgenomics/man/SignalNormalization.Rd MPAgenomics/man/variableSelection.Rd MPAgenomics/man/symmetrizeFracB.Rd MPAgenomics/man/findPlateau.Rd MPAgenomics/man/getFracBSignal.Rd MPAgenomics/man/addData.Rd MPAgenomics/man/createEmptyArchitecture.Rd MPAgenomics/man/MPAgenomics-package.Rd MPAgenomics/man/getCopyNumberSignal.Rd

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