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pathClass (version 0.9.3)

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

0.9.3

License

GPL (>= 2)

Maintainer

Marc Johannes

Last Published

May 5th, 2012

Functions in pathClass (0.9.3)

desummarize.ranks

Desummarize GeneRanks back to the corresponding probesets...
crossval

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

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

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

Calculation of diffusion kernel matrix...
predict.graphSVM

Predict Method for Graph-SVM Fits...
adjacency.matrix

An adjacency matrix of a random graph...
fit.rfe

Recursive Feature Elimination (RFE)...
pathClass-package

Classification with SMVs and prior knowledge
y

Example class labels for the gene expression data...
predict.networkBasedSVM

Predict Method for Network-based SVM Fits...
mapping

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

Summarize probe sets...
as.adjacencyList

Uses a adjacency matrix to create a adjacency list...
fit.rrfe

Reweighted Recursive Feature Elimination (RRFE)...
fit.graph.svm

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

Parse the HPRD flat file...
predict.rfe

Predict Method for RFE Fits...
getGeneRanks

Calculate GeneRanks as used by RRFE...
fit.networkBasedSVM

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

Predict Method for RRFE Fits...
plot.pathClassResult

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

Example gene expression data...