pathClass: Classification using biological pathways as prior knowledge

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pathClass is a collection of classification methods that use information about feature connectivity in a biological network as an additional source of information. This additional knowledge is incorporated into the classification a priori. Several authors have shown that this approach significantly increases the classification performance.

Author
Marc Johannes
Date of publication
2013-07-01 07:43:40
Maintainer
Marc Johannes <JohannesMarc@gmail.com>
License
GPL (>= 2)
Version
0.9.4

View on CRAN

Man pages

adjacency.matrix
An adjacency matrix of a random graph
as.adjacencyList
Uses a adjacency matrix to create a adjacency list
calc.diffusionKernel
Calculation of diffusion kernel matrix
crossval
Performs cross-validation with a specified algorithm
desummarize.ranks
Desummarize GeneRanks back to the corresponding probesets
extractFeatures
Extracts features which have been choosen by the...
fit.graph.svm
Implementation of a supervised classification framework...
fit.networkBasedSVM
Implementation of the network-based Support Vector Machine...
fit.rfe
Recursive Feature Elimination (RFE)
fit.rrfe
Reweighted Recursive Feature Elimination (RRFE)
getGeneRanks
Calculate GeneRanks as used by RRFE
mapping
A mapping of Refseq Protein IDs to probe set IDs for the gene...
matchMatrices
Matches the expression data to the adjacency matrix using the...
pathClass-package
Classification with SMVs and prior knowledge
plot.pathClassResult
Prints the result of one or more cross-validation run(s)
predict.graphSVM
Predict Method for Graph-SVM Fits
predict.networkBasedSVM
Predict Method for Network-based SVM Fits
predict.rfe
Predict Method for RFE Fits
predict.rrfe
Predict Method for RRFE Fits
read.hprd
Parse the HPRD flat file
summarizeProbes
Summarize probe sets
x
Example gene expression data
y
Example class labels for the gene expression data

Files in this package

pathClass
pathClass/MD5
pathClass/vignettes
pathClass/vignettes/references.bib
pathClass/vignettes/pathClass.rnw
pathClass/vignettes/pathClass-benchmark.pdf
pathClass/man
pathClass/man/y.Rd
pathClass/man/x.Rd
pathClass/man/summarizeProbes.Rd
pathClass/man/read.hprd.Rd
pathClass/man/predict.rrfe.Rd
pathClass/man/predict.rfe.Rd
pathClass/man/predict.networkBasedSVM.Rd
pathClass/man/predict.graphSVM.Rd
pathClass/man/plot.pathClassResult.Rd
pathClass/man/pathClass-package.Rd
pathClass/man/matchMatrices.Rd
pathClass/man/mapping.Rd
pathClass/man/getGeneRanks.Rd
pathClass/man/fit.rrfe.Rd
pathClass/man/fit.rfe.Rd
pathClass/man/fit.networkBasedSVM.Rd
pathClass/man/fit.graph.svm.Rd
pathClass/man/extractFeatures.Rd
pathClass/man/desummarize.ranks.Rd
pathClass/man/crossval.Rd
pathClass/man/calc.diffusionKernel.Rd
pathClass/man/as.adjacencyList.Rd
pathClass/man/adjacency.matrix.Rd
pathClass/inst
pathClass/inst/doc
pathClass/inst/doc/pathClass.rnw
pathClass/inst/doc/pathClass.pdf
pathClass/inst/doc/pathClass.R
pathClass/data
pathClass/data/example_data.rda
pathClass/data/adjacency.matrix.RData
pathClass/R
pathClass/R/networkBasedSVM.R
pathClass/R/SpanBound.R
pathClass/R/SVMs.R
pathClass/R/RecursiveFeatureElimination.R
pathClass/R/RRFE.R
pathClass/R/PathwayMethods.R
pathClass/R/GraphSVM.R
pathClass/R/GeneRank.R
pathClass/R/CrossValidation.R
pathClass/NAMESPACE
pathClass/DESCRIPTION