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geNetClassifier (version 1.12.0)

Classify diseases and build associated gene networks using gene expression profiles

Description

Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.

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Version

Version

1.12.0

License

GPL (>= 2)

Maintainer

Last Published

February 15th, 2017

Functions in geNetClassifier (1.12.0)

overview-methods

Overview
genesDetails-methods

Details of the genes in the network.
plotAssignments

Plot assignment probabilities
GeneralizationError-class

Class "GeneralizationError" (slot of GeNetClassifierReturn)
numGenes-methods

Number of genes in the genesRanking.
queryGeNetClassifier

Queries the classifier trained with geNetClassifier.
calculateGenesRanking

Calculate GenesRanking
externalValidation.probMatrix

Probability matrix.
plotExpressionProfiles

Expression profiles plot.
getRanking-methods

Shows the genes ranking.
plot.GeNetClassifierReturn

Plot GeNetClassifierReturn
geNetClassifier

Main function of the geNetClassifier package. Trains the multi-class SVM classifier based on the given gene expression data through transparent detection of gene markers and their associated networks.
plotNetwork

Plot GenesNetwork
gClasses-methods

Classes in the ranking.
getEdges-methods

Edges in the network.
leukemiasClassifier

Sample leukemias classifier
getNumNodes-methods

Number of nodes in the network.
GenesNetwork-class

Class "GenesNetwork"
geNetClassifier-package

classify diseases and build associated gene networks using gene expression profiles
plot.GenesRanking

Plot GenesRanking
externalValidation.stats

Statistics of the external validation.
numSignificantGenes-methods

Number of ranked genes over the posterior probability threshold.
geneSymbols

Gene symbols associated to human Ensemble IDs.
querySummary

Summary of the query.
GenesRanking-class

Class "GenesRanking"
getSubNetwork-methods

Get a sub-network.
getTopRanking-methods

Gets a new ranking with the given top genes.
getNodes-methods

Nodes in the network.
plotDiscriminantPower

Plots the genes' Discriminant Power.
GeNetClassifierReturn-class

Class "GeNetClassifierReturn"
setProperties-methods

Set properties
network2txt

network2txt
getNumEdges-methods

Number of edges in the network.