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pathClass (version 0.8)

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

29

Version

0.8

License

GPL (>= 2)

Maintainer

Marc Johannes

Last Published

November 8th, 2010

Functions in pathClass (0.8)

read.hprd

Parse the HPRD flat file...
mapping

A mapping of Refseq Protein IDs to probe set IDs for the gene expression data...
as.adjacencyList

Uses a adjacency matrix to create a adjacency list...
getGeneRanks

Calculate GeneRanks as used by RRFE...
predict.rfe

Predict Method for RFE Fits...
predict.networkBasedSVM

Predict Method for Network-based SVM Fits...
pathClass-package

Classification with SMVs and prior knowledge
adjacency.matrix

An adjacency matrix of a random graph...
summarizeProbes

Summarize probe sets...
fit.networkBasedSVM

Implementation of the network-based Support Vector Machine introduced by Yanni Zhu et al.
fit.graph.svm

Implementation of a supervised classification framework introduced by Franck Rapaport et al.
x

Example gene expression data...
predict.graphSVM

Predict Method for Graph-SVM Fits...
predict.rrfe

Predict Method for RRFE Fits...
desummarize.ranks

Desummarize GeneRanks back to the corresponding probesets...
fit.rfe

Recursive Feature Elimination (RFE)...
matchMatrices

Matches the expression data to the adjacency matrix using the provided mapping.
calc.diffusionKernel

Calculation of diffusion kernel matrix...
extractFeatures

Extracts features which have been choosen by the classifier(s).
plot.pathClassResult

Prints the result of one or more cross-validation run(s)...
fit.rrfe

Reweighted Recursive Feature Elimination (RRFE)...
crossval

Performs cross-validation with a specified algorithm...
y

Example class labels for the gene expression data...