gkmSVM: Gapped-Kmer Support Vector Machine
Version 0.71.0

Imports the 'gkmSVM' v2.0 functionalities into R (www.beerlab.org/gkmsvm). It also uses the 'kernlab' library (separate R package by different authors) for various SVM algorithms.

AuthorMahmoud Ghandi
Date of publication2016-07-19 10:38:07
MaintainerMahmoud Ghandi <mghandi@gmail.com>
LicenseGPL (>= 2)
Version0.71.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("gkmSVM")

Getting started

Package overview

Popular man pages

genNullSeqs: Generating GC/repeat matched randomly selected genomic...
gkmsvm_classify: Classifying(/scoring) new sequences using the gkmSVM model
gkmsvm_delta: Calculating deltaSVM scores
gkmsvm_kernel: Computing the kernel matrix
gkmSVM-package: Gapped-Kmer Support Vector Machine
gkmsvm_train: Training the SVM model
gkmsvm_trainCV: Training the SVM model, using repeated CV to tune parameter C...
See all...

All man pages Function index File listing

Man pages

genNullSeqs: Generating GC/repeat matched randomly selected genomic...
gkmsvm_classify: Classifying(/scoring) new sequences using the gkmSVM model
gkmsvm_delta: Calculating deltaSVM scores
gkmsvm_kernel: Computing the kernel matrix
gkmSVM-package: Gapped-Kmer Support Vector Machine
gkmsvm_train: Training the SVM model
gkmsvm_trainCV: Training the SVM model, using repeated CV to tune parameter C...

Functions

genNullSeqs Man page Source code
gkmSVM Man page
gkmSVM-package Man page
gkmsvm_classify Man page Source code Source code
gkmsvm_delta Man page Source code
gkmsvm_kernel Man page Source code Source code
gkmsvm_train Man page Source code
gkmsvm_trainCV Man page Source code

Files

src
src/SequenceData.cpp
src/gkmCommonLib.cpp
src/CiDLPasses.cpp
src/GTreeLeafData2.h
src/GTree.cpp
src/Sequence.h
src/gkmsvm_kernel.cpp
src/CiDLPasses.h
src/LList.cpp
src/CountKLmers.h
src/CountKLmersH.cpp
src/EstimLogRatio.h
src/CountKLmers.cpp
src/CalcWmML.cpp
src/LList.h
src/MLEstimKLmers.h
src/globalvar.h
src/MLEstimKLmersLog.cpp
src/global.cpp
src/LKTree.cpp
src/KLmer.cpp
src/GTreeLeafData2.cpp
src/CbinMMtable.h
src/Converter.cpp
src/SVMtrain.cpp
src/GTreeLeafData.h
src/GTree.h
src/EstimLogRatio.cpp
src/SVMtrain.h
src/SequenceNames.cpp
src/LTree.cpp
src/SequenceData.h
src/Converter.h
src/MLEstimKLmers.cpp
src/CountKLmersGeneral.h
src/KLmer.h
src/CbinMMtree.cpp
src/LKTree.h
src/mainSVMclassify.cpp
src/LTreef.cpp
src/MLEstimKLmersLog.h
src/mainSVMtrain.cpp
src/Sequence.cpp
src/LTreeS.h
src/global.h
src/GTree2.cpp
src/LTree.h
src/GTree2.h
src/CbinMMtable.cpp
src/mainGkmKernel.cpp
src/RcppExports.cpp
src/LTreef.h
src/CountKLmersH.h
src/CbinMMtree.h
src/globalTypeDefs.h
src/LTreeS.cpp
src/gkmsvm_classify.cpp
src/CalcWmML.h
src/GTreeLeafData.cpp
src/CountKLmersGeneral.cpp
src/SequenceNames.h
NAMESPACE
R
R/gkmsvm_delta.R
R/genNullSeqs.R
R/RcppExports.R
R/gkmsvm_kernel.R
R/gkmsvm_train.R
R/gkmsvm_classify.R
R/gkmsvm_trainCV.R
MD5
DESCRIPTION
man
man/gkmsvm_trainCV.Rd
man/gkmSVM-package.Rd
man/gkmsvm_classify.Rd
man/gkmsvm_train.Rd
man/gkmsvm_kernel.Rd
man/gkmsvm_delta.Rd
man/genNullSeqs.Rd
gkmSVM documentation built on May 19, 2017, 10:46 a.m.

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