pathClass v0.9.2

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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
mapping A mapping of Refseq Protein IDs to probe set IDs for the gene expression data...
read.hprd Parse the HPRD flat file...
pathClass-package Classification with SMVs and prior knowledge
as.adjacencyList Uses a adjacency matrix to create a adjacency list...
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.
matchMatrices Matches the expression data to the adjacency matrix using the provided mapping.
x Example gene expression data...
getGeneRanks Calculate GeneRanks as used by RRFE...
desummarize.ranks Desummarize GeneRanks back to the corresponding probesets...
predict.rfe Predict Method for RFE Fits...
fit.rrfe Reweighted Recursive Feature Elimination (RRFE)...
predict.networkBasedSVM Predict Method for Network-based SVM Fits...
fit.networkBasedSVM Implementation of the network-based Support Vector Machine introduced by Yanni Zhu et al.
adjacency.matrix An adjacency matrix of a random graph...
calc.diffusionKernel Calculation of diffusion kernel matrix...
plot.pathClassResult Prints the result of one or more cross-validation run(s)...
summarizeProbes Summarize probe sets...
y Example class labels for the gene expression data...
fit.rfe Recursive Feature Elimination (RFE)...
predict.rrfe Predict Method for RRFE Fits...
predict.graphSVM Predict Method for Graph-SVM Fits...
crossval Performs cross-validation with a specified algorithm...
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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 2011-02-08 11:52:16 UTC; marc
Repository CRAN
Date/Publication 2011-02-08 15:51:00

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