pathClass v0.9.1

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by Marc Johannes

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

Type Package
Date 2010-02-25
License GPL (>= 2)
LazyLoad yes
Collate 'CrossValidation.R' 'GeneRank.R' 'GraphSVM.R' 'networkBasedSVM.R' 'PathwayMethods.R' 'RecursiveFeatureElimination.R' 'RRFE.R' 'SpanBound.R' 'SVMs.R'
Packaged 2011-01-18 10:33:11 UTC; marc
Repository CRAN
Date/Publication 2011-01-18 14:47:22

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