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pathClass (version 0.5)

Classification using biological pathways as prior knowledge

Description

pathClass is a collection of classification methods that use information about how features are connected in the underlying 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

0.5

License

GPL (>= 2)

Maintainer

Marc Johannes

Last Published

September 27th, 2010

Functions in pathClass (0.5)

fit.networkBasedSVM

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

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

Summarize probe sets...
desummarize.ranks

Desummarize GeneRanks back to the corresponding probesets...
read.hprd

Parse the HPRD flat file...
matchMatrices

Matches the expression data to the adjacency matrix using the provided mapping.
fit.rfe

Recursive Feature Elimination (RFE)...
calc.diffusionKernel

Calculation of diffusion kernel matrix...
crossval

Performs cross-validation with a specified algorithm...
fit.rrfe

Reweighted Recursive Feature Elimination (RRFE)...
pathClass-package

Classification with SMVs and prior knowledge
fit.graph.svm

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

An adjacency matrix of a random graph...
as.adjacencyList

Uses a adjacency matrix to create a adjacency list...
plot.pathClassResult

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