MPAgenomics: Multi-Patient Analysis of Genomic Markers

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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.

Author
Quentin 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 publication
2015-09-09 15:03:13
Maintainer
Samuel Blanck <samuel.blanck@inria.fr>
License
GPL(>=2)
Version
1.1.4

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Man pages

addChipType
Add a new chip type to the existing aroma architecture
addData
Add a new data-set to the existing aroma architecture
callingObject
Create the list of parameters for callingProcess function
callingProcess
Calling aberrations in segmented copy-number signal.
CNAobjectToCGHcallObject
Convert CNAobject
cnSegCallingProcess
Segment a copy-number signal and call the found segments.
createArchitecture
Create aroma architecture and copy files
createEmptyArchitecture
Create aroma architecture
filterSeg
Filter segments
findPlateau
Find the best choice of segmentation parameter.
getCopyNumberSignal
Extract copy-number signal from aroma files
getFracBSignal
Extract allele B fraction signal from aroma files
getGenotypeCalls
Extract genotype calls from aroma files
getListOfFiles
Get the contents of a data folder
getSymFracBSignal
Extract symmetrized allele B fraction signal from aroma files
HDlarsbivariate
lars algorithm for bivariate signal
markerSelection
markers selection
MPAgenomics-package
Multi-Patient Analysis of Genomic Markers
segFracBSignal
segmentation function for the allele B fraction
segmentation
segmentation function
segmentationAroma
segmentation function
segmentationObject
Create the list of parameters for segmentation function
SignalNormalization
Normalization process
signalPreProcess
Normalization process
symmetrizeFracB
symmetrize an allele B fraction signal
variableSelection
SNPs selection

Files in this package

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