Classification using biological pathways as prior knowledge


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Documentation for package ‘pathClass’ version 0.9.4

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pathClass-package Classification with SMVs and prior knowledge
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 classifier(s).
fit.graph.svm Implementation of a supervised classification framework introduced by Franck Rapaport et al., 2007.
fit.networkBasedSVM Implementation of the network-based Support Vector Machine introduced by Yanni Zhu et al., 2009.
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 expression data
matchMatrices Matches the expression data to the adjacency matrix using the provided mapping.
pathClass 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