gkmSVM: Gapped-Kmer Support Vector Machine

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.

Author
Mahmoud Ghandi
Date of publication
2016-07-19 10:38:07
Maintainer
Mahmoud Ghandi <mghandi@gmail.com>
License
GPL (>= 2)
Version
0.71.0

View on CRAN

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...

Files in this package

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