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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("geNetClassifier")
AuthorSara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain.
Bioconductor views Classification DifferentialExpression Microarray
Date of publicationNone
MaintainerSara Aibar <saibar@usal.es>
LicenseGPL (>= 2)
Version1.16.0
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

Functions

calculateGenesRanking Man page
edges,GenesNetwork-method Man page
edges,GenesNetwork-method Man page
externalValidation.probMatrix Man page
externalValidation.stats Man page
extractGenes,GenesRanking-method Man page
gClasses Man page
gClasses,GenesRanking-method Man page
gClasses,GenesRanking-method Man page
gClasses-methods Man page
GeneralizationError Man page
GeneralizationError-class Man page
genesDetails Man page
genesDetails.GenesRanking Man page
genesDetails,GenesRanking-method Man page
genesDetails,GenesRanking-method Man page
genesDetails-methods Man page
GenesNetwork Man page
GenesNetwork-class Man page
GenesRanking Man page
GenesRanking-class Man page
geneSymbols Man page
geNetClassifier Man page
geNetClassifier-package Man page
GeNetClassifierReturn Man page
GeNetClassifierReturn-class Man page
getEdges Man page
getEdges,GenesNetwork-method Man page
getEdges,GenesNetwork-method Man page
getEdges-methods Man page
getNodes Man page
getNodes,GenesNetwork-method Man page
getNodes,GenesNetwork-method Man page
getNodes-methods Man page
getNumEdges Man page
getNumEdges,GenesNetwork-method Man page
getNumEdges,GenesNetwork-method Man page
getNumEdges-methods Man page
getNumNodes Man page
getNumNodes,GenesNetwork-method Man page
getNumNodes,GenesNetwork-method Man page
getNumNodes-methods Man page
getRanking Man page
getRanking.GenesRanking Man page
getRanking,GenesRanking-method Man page
getRanking,GenesRanking-method Man page
getRanking-methods Man page
getSlots,GeNetClassifierReturn-method Man page
getSubNetwork Man page
getSubNetwork,GenesNetwork-method Man page
getSubNetwork,GenesNetwork-method Man page
getSubNetwork,GeNetClassifierReturn-method Man page
getSubNetwork,list-method Man page
getSubNetwork-methods Man page
getSubNetwork,NULL-method Man page
getTopRanking Man page
getTopRanking.GenesRanking Man page
getTopRanking,GenesRanking-method Man page
getTopRanking,GenesRanking-method Man page
getTopRanking-methods Man page
initialize,GeneralizationError-method Man page
initialize,GenesNetwork-method Man page
initialize,GenesRanking-method Man page
initialize,GeNetClassifierReturn-method Man page
leukemiasClassifier Man page
names,GeNetClassifierReturn-method Man page
network2txt Man page
network2txt,GenesNetwork-method Man page
network2txt,list-method Man page
network2txt-methods Man page
nGenes,GenesRanking-method Man page
nodes,GenesNetwork-method Man page
nodes,GenesNetwork-method Man page
numEdges,GenesNetwork-method Man page
numEdges,GenesNetwork-method Man page
numGenes Man page
numGenes,GenesRanking-method Man page
numGenes-methods Man page
numNodes,GenesNetwork-method Man page
numNodes,GenesNetwork-method Man page
numSignificantGenes Man page
numSignificantGenes.GenesRanking Man page
numSignificantGenes,GenesRanking-method Man page
numSignificantGenes,GenesRanking-method Man page
numSignificantGenes-methods Man page
overview Man page
overview,GeneralizationError-method Man page
overview,GeneralizationError-method Man page
overview,GenesNetwork-method Man page
overview,GenesNetwork-method Man page
overview,GenesRanking-method Man page
overview,GenesRanking-method Man page
overview,GeNetClassifierReturn-method Man page
overview,GeNetClassifierReturn-method Man page
overview-methods Man page
plotAssignments Man page
plotDiscriminantPower Man page
plotExpressionProfiles Man page
plot.GenesNetwork Man page
plot,GenesNetwork-method Man page
plotGenesRanking Man page
plot.GenesRanking Man page
plot,GenesRanking-method Man page
plot,GenesRanking,missing-method Man page
plotGeNetClassifierReturn Man page
plot.GeNetClassifierReturn Man page
plotGeNetClassifierReturn,GeNetClassifierReturn-method Man page
plot,GeNetClassifierReturn-method Man page
plotNetwork Man page
plotNetwork,GenesNetwork-method Man page
queryGeNetClassifier Man page
querySummary Man page
setProperties Man page
setProperties.GenesRanking Man page
setProperties,GenesRanking-method Man page
setProperties,GenesRanking-method Man page
setProperties-methods Man page
show,GeneralizationError-method Man page
show,GenesNetwork-method Man page
show,GenesRanking-method Man page
show,GeNetClassifierReturn-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.