PMA: Penalized Multivariate Analysis

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Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis, described in the following papers: (1) Witten, Tibshirani and Hastie (2009) A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10(3):515-534. (2) Witten and Tibshirani (2009) Extensions of sparse canonical correlation analysis, with applications to genomic data. Statistical Applications in Genetics and Molecular Biology 8(1): Article 28.

Author
Daniela Witten and Rob Tibshirani and Sam Gross and Balasubramanian Narasimhan
Date of publication
2013-03-25 08:26:26
Maintainer
Daniela Witten <dwitten@u.washington.edu>
License
GPL (>= 2)
Version
1.0.9

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Man pages

breastdata
Breast cancer gene expression + DNA copy number data set from...
CCA
Perform sparse canonical correlation analysis using the...
CCA.permute
Select tuning parameters for sparse canonical correlation...
MultiCCA
Perform sparse multiple canonical correlation analysis.
MultiCCA.permute
Select tuning parameters for sparse multiple canonical...
notusing/CCA
Perform sparse canonical correlation analysis using the...
notusing/CCA.permute
Select tuning parameters for sparse canonical correlation...
PlotCGH
Plot CGH data
PMA-internal
Internal PMA functions
PMA-package
Penalized Multivariate Analysis
PMD
Get a penalized matrix decomposition for a data matrix.
PMD.cv
Do tuning parameter selection for PMD via cross-validation
SPC
Perform sparse principal component analysis
SPC.cv
Perform cross-validation on sparse principal component...

Files in this package

PMA
PMA/MD5
PMA/R
PMA/R/CCA.xlfuns.R
PMA/R/zzz.R
PMA/R/SamrFunctions.R
PMA/R/PMD.R
PMA/R/PlotFusedLasso.R
PMA/R/CCA.R
PMA/R/FLSAGeneralInclude.R
PMA/R/MultiCCA.R
PMA/R/PMD.CGH.R
PMA/src
PMA/src/Groups.h
PMA/src/init.cc
PMA/src/FLSAGeneralMain.cc
PMA/src/Scheduler.cc
PMA/src/FLSA.h
PMA/src/GeneralFunctions.cc
PMA/src/PenaltyGraph.h
PMA/src/Groups.cc
PMA/src/PenaltyGraph.cc
PMA/src/FLSAGeneral.cc
PMA/src/MaxFlowGraph.cc
PMA/src/GraphDefinitions.h
PMA/src/FLSA.cc
PMA/src/FLSAGeneral.h
PMA/src/Scheduler.h
PMA/src/GeneralFunctions.h
PMA/src/MaxFlowGraph.h
PMA/data
PMA/data/breastdata.rda
PMA/data/datalist
PMA/NAMESPACE
PMA/DESCRIPTION
PMA/man
PMA/man/SPC.Rd
PMA/man/notusing
PMA/man/notusing/CCA.Rd
PMA/man/notusing/CCA.permute.Rd
PMA/man/MultiCCA.Rd
PMA/man/SPC.cv.Rd
PMA/man/PMA-package.Rd
PMA/man/CCA.Rd
PMA/man/PMD.Rd
PMA/man/breastdata.Rd
PMA/man/PlotCGH.Rd
PMA/man/PMA-internal.Rd
PMA/man/MultiCCA.permute.Rd
PMA/man/CCA.permute.Rd
PMA/man/PMD.cv.Rd