pathClass v0.9.4

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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
extractFeatures Extracts features which have been choosen by the classifier(s).
fit.rrfe Reweighted Recursive Feature Elimination (RRFE)
predict.graphSVM Predict Method for Graph-SVM Fits
matchMatrices Matches the expression data to the adjacency matrix using the provided mapping.
predict.rrfe Predict Method for RRFE Fits
fit.rfe Recursive Feature Elimination (RFE)
summarizeProbes Summarize probe sets
predict.rfe Predict Method for RFE Fits
desummarize.ranks Desummarize GeneRanks back to the corresponding probesets
predict.networkBasedSVM Predict Method for Network-based SVM Fits
calc.diffusionKernel Calculation of diffusion kernel matrix
mapping A mapping of Refseq Protein IDs to probe set IDs for the gene expression data
fit.graph.svm Implementation of a supervised classification framework introduced by Franck Rapaport et al., 2007.
pathClass-package Classification with SMVs and prior knowledge
fit.networkBasedSVM Implementation of the network-based Support Vector Machine introduced by Yanni Zhu et al., 2009.
plot.pathClassResult Prints the result of one or more cross-validation run(s)
adjacency.matrix An adjacency matrix of a random graph
crossval Performs cross-validation with a specified algorithm
as.adjacencyList Uses a adjacency matrix to create a adjacency list
y Example class labels for the gene expression data
read.hprd Parse the HPRD flat file
x Example gene expression data
getGeneRanks Calculate GeneRanks as used by RRFE
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Vignettes of pathClass

Name
pathClass-benchmark.pdf
pathClass.rnw
references.bib
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Details

Type Package
Date 2013-06-25
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 2013-06-29 11:48:33 UTC; mj
Repository CRAN
Date/Publication 2013-07-01 07:43:40
NeedsCompilation no

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