pathClass v0.9.1
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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 | |
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 |
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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