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 |

**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

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

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