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pathClass (version 0.9.2)

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

0.9.2

License

GPL (>= 2)

Maintainer

Marc Johannes

Last Published

February 8th, 2011

Functions in pathClass (0.9.2)

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...