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pathClass (version 0.9.4)

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

12

Version

0.9.4

License

GPL (>= 2)

Maintainer

Marc Johannes

Last Published

July 1st, 2013

Functions in pathClass (0.9.4)

extractFeatures

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

Reweighted Recursive Feature Elimination (RRFE)
predict.graphSVM

Predict Method for Graph-SVM Fits
matchMatrices

Matches the expression data to the adjacency matrix using the provided mapping.
predict.rrfe

Predict Method for RRFE Fits
fit.rfe

Recursive Feature Elimination (RFE)
summarizeProbes

Summarize probe sets
predict.rfe

Predict Method for RFE Fits
desummarize.ranks

Desummarize GeneRanks back to the corresponding probesets
predict.networkBasedSVM

Predict Method for Network-based SVM Fits
calc.diffusionKernel

Calculation of diffusion kernel matrix
mapping

A mapping of Refseq Protein IDs to probe set IDs for the gene expression data
fit.graph.svm

Implementation of a supervised classification framework introduced by Franck Rapaport et al., 2007.
pathClass-package

Classification with SMVs and prior knowledge
fit.networkBasedSVM

Implementation of the network-based Support Vector Machine introduced by Yanni Zhu et al., 2009.
plot.pathClassResult

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

An adjacency matrix of a random graph
crossval

Performs cross-validation with a specified algorithm
as.adjacencyList

Uses a adjacency matrix to create a adjacency list
y

Example class labels for the gene expression data
read.hprd

Parse the HPRD flat file
x

Example gene expression data
getGeneRanks

Calculate GeneRanks as used by RRFE