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pathClass (version 0.9.1)

Classification using biological pathways as prior knowledge

Description

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.

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Version

Install

install.packages('pathClass')

Monthly Downloads

50

Version

0.9.1

License

GPL (>= 2)

Maintainer

Marc Johannes

Last Published

January 18th, 2011

Functions in pathClass (0.9.1)

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).