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