Learn R Programming

⚠️There's a newer version (0.9.4) of this package.Take me there.

pathClass (version 0.7)

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.

Copy Link

Version

Install

install.packages('pathClass')

Monthly Downloads

29

Version

0.7

License

GPL (>= 2)

Maintainer

Marc Johannes

Last Published

November 3rd, 2010

Functions in pathClass (0.7)

crossval

Performs cross-validation with a specified algorithm...
as.adjacencyList

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

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

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

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

Classification with SMVs and prior knowledge
summarizeProbes

Summarize probe sets...
matchMatrices

Matches the expression data to the adjacency matrix using the provided mapping.
x

Example gene expression data...
fit.graph.svm

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

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

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

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

Reweighted Recursive Feature Elimination (RRFE)...
desummarize.ranks

Desummarize GeneRanks back to the corresponding probesets...
adjacency.matrix

An adjacency matrix of a random graph...
read.hprd

Parse the HPRD flat file...
calc.diffusionKernel

Calculation of diffusion kernel matrix...