pathClass v0.9.2
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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 | |
| 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 |
| depends | affy , base (>= 2.9.0) , Biobase , igraph , kernlab , lpSolve , R (>= 2.9.0) , ROCR , svmpath |
| suggests | golubEsets , hu6800 , hu6800.db |
| enhances | multicore |
| Contributors | Marc Johannes |
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