# pathClass v0.9.3

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## Classification using biological pathways as prior knowledge

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.

## Functions in pathClass

 Name Description desummarize.ranks Desummarize GeneRanks back to the corresponding probesets... crossval Performs cross-validation with a specified algorithm... extractFeatures Extracts features which have been choosen by the classifier(s). matchMatrices Matches the expression data to the adjacency matrix using the provided mapping. calc.diffusionKernel Calculation of diffusion kernel matrix... predict.graphSVM Predict Method for Graph-SVM Fits... adjacency.matrix An adjacency matrix of a random graph... fit.rfe Recursive Feature Elimination (RFE)... pathClass-package Classification with SMVs and prior knowledge y Example class labels for the gene expression data... predict.networkBasedSVM Predict Method for Network-based SVM Fits... mapping A mapping of Refseq Protein IDs to probe set IDs for the gene expression data... summarizeProbes Summarize probe sets... as.adjacencyList Uses a adjacency matrix to create a adjacency list... fit.rrfe Reweighted Recursive Feature Elimination (RRFE)... fit.graph.svm Implementation of a supervised classification framework introduced by Franck Rapaport et al. read.hprd Parse the HPRD flat file... predict.rfe Predict Method for RFE Fits... getGeneRanks Calculate GeneRanks as used by RRFE... fit.networkBasedSVM Implementation of the network-based Support Vector Machine introduced by Yanni Zhu et al. predict.rrfe Predict Method for RRFE Fits... plot.pathClassResult Prints the result of one or more cross-validation run(s)... x Example gene expression data... No Results!