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gkmSVM (version 0.83.0)

Gapped-Kmer Support Vector Machine

Description

Imports the 'gkmSVM' v2.0 functionalities into R It also uses the 'kernlab' library (separate R package by different authors) for various SVM algorithms. Users should note that the suggested packages 'rtracklayer', 'GenomicRanges', 'BSgenome', 'BiocGenerics', 'Biostrings', 'GenomeInfoDb', 'IRanges', and 'S4Vectors' are all BioConductor packages .

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Version

Install

install.packages('gkmSVM')

Monthly Downloads

256

Version

0.83.0

License

GPL (>= 2)

Maintainer

Mike Beer

Last Published

August 20th, 2023

Functions in gkmSVM (0.83.0)

gkmsvm_classify

Classifying(/scoring) new sequences using the gkmSVM model
gkmsvm_kernel

Computing the kernel matrix
gkmsvm_train

Training the SVM model
gkmsvm_trainCV

Training the SVM model, using repeated CV to tune parameter C and plot ROC curves
genNullSeqs

Generating GC/repeat matched randomly selected genomic sequences for the negative set
gkmSVM-package

Gapped-Kmer Support Vector Machine
gkmsvm_delta

Calculating deltaSVM scores