geNetClassifier: Classify diseases and build associated gene networks using gene expression profiles

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.

AuthorSara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain.
Date of publicationNone
MaintainerSara Aibar <saibar@usal.es>
LicenseGPL (>= 2)
Version1.14.0
http://www.cicancer.org

View on Bioconductor

Man pages

calculateGenesRanking: Calculate GenesRanking

externalValidation.probMatrix: Probability matrix.

externalValidation.stats: Statistics of the external validation.

gClasses-methods: Classes in the ranking.

GeneralizationError-class: Class "GeneralizationError" (slot of GeNetClassifierReturn)

genesDetails-methods: Details of the genes in the network.

GenesNetwork-class: Class "GenesNetwork"

GenesRanking-class: Class "GenesRanking"

geneSymbols: Gene symbols associated to human Ensemble IDs.

geNetClassifier: Main function of the geNetClassifier package. Trains the...

geNetClassifier-package: classify diseases and build associated gene networks using...

GeNetClassifierReturn-class: Class "GeNetClassifierReturn"

getEdges-methods: Edges in the network.

getNodes-methods: Nodes in the network.

getNumEdges-methods: Number of edges in the network.

getNumNodes-methods: Number of nodes in the network.

getRanking-methods: Shows the genes ranking.

getSubNetwork-methods: Get a sub-network.

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

leukemiasClassifier: Sample leukemias classifier

network2txt: network2txt

numGenes-methods: Number of genes in the genesRanking.

numSignificantGenes-methods: Number of ranked genes over the posterior probability...

overview-methods: Overview

plotAssignments: Plot assignment probabilities

plotDiscriminantPower: Plots the genes' Discriminant Power.

plotExpressionProfiles: Expression profiles plot.

plot.GenesRanking: Plot GenesRanking

plot.GeNetClassifierReturn: Plot GeNetClassifierReturn

plotNetwork: Plot GenesNetwork

queryGeNetClassifier: Queries the classifier trained with geNetClassifier.

querySummary: Summary of the query.

setProperties-methods: Set properties

Files in this package

geNetClassifier/DESCRIPTION
geNetClassifier/NAMESPACE
geNetClassifier/NEWS
geNetClassifier/R
geNetClassifier/R/class.GeNetClassifierReturn.R geNetClassifier/R/class.GeneralizationError.R geNetClassifier/R/class.GenesNetwork.R geNetClassifier/R/class.GenesRanking.R geNetClassifier/R/function.main.R geNetClassifier/R/functions.private.R geNetClassifier/R/functions.public.R
geNetClassifier/build
geNetClassifier/build/vignette.rds
geNetClassifier/data
geNetClassifier/data/datalist
geNetClassifier/data/geneSymbols.RData
geNetClassifier/data/leukemiasClassifier.RData
geNetClassifier/inst
geNetClassifier/inst/CITATION
geNetClassifier/inst/doc
geNetClassifier/inst/doc/geNetClassifier-vignette.R
geNetClassifier/inst/doc/geNetClassifier-vignette.Rnw
geNetClassifier/inst/doc/geNetClassifier-vignette.pdf
geNetClassifier/inst/unitTests
geNetClassifier/inst/unitTests/test_externalValidationStats.R
geNetClassifier/inst/unitTests/test_geNetClassifier.R
geNetClassifier/inst/unitTests/test_plotExpressionProfiles.R
geNetClassifier/man
geNetClassifier/man/GeNetClassifierReturn-class.Rd geNetClassifier/man/GeneralizationError-class.Rd geNetClassifier/man/GenesNetwork-class.Rd geNetClassifier/man/GenesRanking-class.Rd geNetClassifier/man/calculateGenesRanking.Rd geNetClassifier/man/externalValidation.probMatrix.Rd geNetClassifier/man/externalValidation.stats.Rd geNetClassifier/man/gClasses-methods.Rd geNetClassifier/man/geNetClassifier-package.Rd geNetClassifier/man/geNetClassifier.Rd geNetClassifier/man/geneSymbols.Rd geNetClassifier/man/genesDetails-methods.Rd geNetClassifier/man/getEdges-methods.Rd geNetClassifier/man/getNodes-methods.Rd geNetClassifier/man/getNumEdges-methods.Rd geNetClassifier/man/getNumNodes-methods.Rd geNetClassifier/man/getRanking-methods.Rd geNetClassifier/man/getSubNetwork-methods.Rd geNetClassifier/man/getTopRanking-methods.Rd geNetClassifier/man/leukemiasClassifier.Rd geNetClassifier/man/network2txt.Rd geNetClassifier/man/numGenes-methods.Rd geNetClassifier/man/numSignificantGenes-methods.Rd geNetClassifier/man/overview-methods.Rd geNetClassifier/man/plot.GeNetClassifierReturn.Rd geNetClassifier/man/plot.GenesRanking.Rd geNetClassifier/man/plotAssignments.Rd geNetClassifier/man/plotDiscriminantPower.Rd geNetClassifier/man/plotExpressionProfiles.Rd geNetClassifier/man/plotNetwork.Rd geNetClassifier/man/queryGeNetClassifier.Rd geNetClassifier/man/querySummary.Rd geNetClassifier/man/setProperties-methods.Rd
geNetClassifier/tests
geNetClassifier/tests/runTests.R
geNetClassifier/vignettes
geNetClassifier/vignettes/Fig11plotNtwALL9g.png
geNetClassifier/vignettes/Fig12plotNtwAML30g.png
geNetClassifier/vignettes/Fig13plotNtwAML100g.pdf
geNetClassifier/vignettes/Fig1intro.png
geNetClassifier/vignettes/Fig2significantGeneswithoutNoL.pdf
geNetClassifier/vignettes/Fig3overlap.png
geNetClassifier/vignettes/Fig4-5geneSelection.pdf
geNetClassifier/vignettes/Fig6leukemiasClassifierAssingorNotAssing.pdf
geNetClassifier/vignettes/Fig7significantGenes.pdf
geNetClassifier/vignettes/Fig8expressionProfilePlot_2g.pdf
geNetClassifier/vignettes/Fig9expressionProfilePlot_B.pdf
geNetClassifier/vignettes/geNetClassifier-vignette.Rnw

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