MineICA: Analysis of an ICA decomposition obtained on genomics data
Version 1.16.0

The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.

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AuthorAnne Biton
Bioconductor views MultipleComparison Visualization
Date of publicationNone
MaintainerAnne Biton <anne.biton@gmail.com>
LicenseGPL-2
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MineICA")

Man pages

A: Retrieve and set Source S and Mixing matrix A from IcaSet
addGenesToGoReport: Add Symbol IDs to hyperGTest results
Alist: Retrieve sample contributions stored in an 'IcaSet' object as...
annot2Color: Association of a colour with each annotation level
annotCarbayo: Carbayo annotation data
annotFeatures: Annotation of features using an annotation package
annotFeaturesComp: Features annotation
annotFeaturesWithBiomaRt: Annotation of features using 'biomaRt'
annotInGene: Features annotation of an object of class IcaSet.
annotReciprocal: annotReciprocal
buildIcaSet: This function builds an object of class 'IcaSet'.
buildMineICAParams: Creates an object of class MineICAParams
build_sortHeatmap: Build the heatmap matrices
class-IcaSet: Class to Contain and Describe an ICA decomposition of...
class-MineICAParams: Class to contain parameters for the analysis of an ICA...
clusterFastICARuns: Run of fastICA and JADE algorithms
clusterSamplesByComp: Cluster samples from an IcaSet
clusterSamplesByComp_multiple: Cluster samples from an IcaSet
clusVarAnalysis: Tests association between clusters of samples and variables
compareAn: Comparison of IcaSet objects using correlation
compareAn2graphfile: compareAn2graphfile
compareGenes: Union and intersection of contributing genes
cor2An: Correlation between two matrices
correl2Comp: correl2Comp
dat: Retrieve and set data from IcaSet
dataCarbayo: Carbayo expression data
doEnrichment: Runs enrichment analysis of contributing genes
getComp: Retrieve feature and sample values on a component stored in...
getProj: Extract projection values
getSdExpr: getSdExpr
hgOver: Output of 'hyperGtest'
hypergeoAn: Runs an enrichment analysis per component using package...
icaSetCarbayo: IcaSet-object containing a FastICA decomposition of gene...
icaSetKim: IcaSet-object containing a FastICA decomposition of gene...
icaSetRiester: IcaSet-object containing a FastICA decomposition of gene...
icaSetStransky: IcaSet-object containing a FastICA decomposition of gene...
indComp: Retrieve and set component labels, indices, and witness genes...
mergeGostatsResults: Merge enrichment results obtained for different databases...
nbOccByGeneInComp: nbOccByGeneInComp
nbOccInComp: Select components the features contribute to
nbOccInComp_simple: nbOccInComp_simple
nodeAttrs: Generate node attributes
plotAllMix: Plots the Gaussian fitted by 'Mclust' on several numeric...
plotCorGraph: Plots graph using
plotDens2classInComp_plotOnly: Plots the densities or boxplots of the component...
plotDensAllAnnotInAllComp: Tests if groups of samples are differently distributed on the...
plotDensOneAnnotInAllComp: Tests if groups of samples are differently distributed on the...
plot_heatmapsOnSel: Plot heatmap associated with each component
plotMclust: Plots the Gaussian fitted by 'Mclust'
plotMix: Plots an histogram and Gaussian fitted by 'Mclust'
plotPosAnnotInComp: Histograms of sample contributions for each annotation level
plotPosOneAnnotInComp_ggplot: Tests if groups of samples are differently distributed on the...
plotPosOneAnnotLevInComp_ggplot: Plots the position of a subset of samples in the histogram of...
plotPosSamplesInComp: Histograms of sample subsets
qualVarAnalysis: Tests association between qualitative variables and...
quantVarAnalysis: Correlation between variables and components.
readA: read A
readS: read S
relativePath: Relative path
runAn: Run analysis of an IcaSet object
runCompareIcaSets: runCompareIcaSets
runEnrich: Enrichment analysis through GOstats
runICA: Run of fastICA and JADE algorithms
selectContrib: Select contributing features/genes
selectFeatures_IQR: Selection of features based on their IQR
selectWitnessGenes: selectWitnessGenes
Slist: Retrieve feature/gene projections stored in an 'IcaSet'...
wilcoxOrKruskalOnA: Comparison of distributions of sample groups
writeGenes: Description of features using package 'biomaRt'.
writeGostatsHtmltable: Writes enrichment results in a HTML file
writeHtmlResTestsByAnnot: Tests if groups of samples are differently distributed on the...
writeProjByComp: writeProjByComp
writeRnkFiles: Write rnk files containing gene projections

Functions

A Man page
A,IcaSet-method Man page
A<- Man page
A<-,IcaSet,data.frame-method Man page
A<-,IcaSet-method Man page
Afile Man page
Afile,MineICAParams-method Man page
Afile<- Man page
Afile<-,MineICAParams,character-method Man page
Afile<-,MineICAParams-method Man page
Alist Man page
Alist,IcaSet-method Man page
IcaSet Man page
IcaSet-class Man page
MineICAParams Man page
MineICAParams-class Man page
S Man page
S,IcaSet-method Man page
S<- Man page
S<-,IcaSet,data.frame-method Man page
S<-,IcaSet-method Man page
SByGene Man page
SByGene,IcaSet-method Man page
SByGene<- Man page
SByGene<-,IcaSet,data.frame-method Man page
SByGene<-,IcaSet-method Man page
Sfile Man page
Sfile,MineICAParams-method Man page
Sfile<- Man page
Sfile<-,MineICAParams,character-method Man page
Sfile<-,MineICAParams-method Man page
Slist Man page
Slist,IcaSet-method Man page
SlistByGene Man page
SlistByGene,IcaSet-method Man page
[ Man page Man page Man page
[,ANY,ANY,ANY,MineICAParams-method Man page
[,ANY,ANY,IcaSet-method Man page Man page
[,ANY,ANY,MineICAParams-method Man page
[,ANY,MineICAParams-method Man page
[,IcaSet,ANY,ANY,ANY-method Man page Man page
[,IcaSet,ANY,ANY-method Man page Man page
[,IcaSet,ANY-method Man page Man page
[,MineICAParams,ANY,ANY,ANY-method Man page
[,MineICAParams,ANY,ANY-method Man page
[,MineICAParams,ANY-method Man page
[<- Man page Man page Man page
[<-,IcaSet,ANY,ANY,ANY,ANY-method Man page Man page
[<-,IcaSet,ANY,ANY,ANY-method Man page Man page
[<-,IcaSet,ANY,ANY-method Man page Man page
[<-,MineICAParams,ANY,ANY,ANY,ANY-method Man page
[<-,MineICAParams,ANY,ANY,ANY-method Man page
[<-,MineICAParams,ANY,ANY-method Man page
[<-,MineICAparams,ANY-method Man page
addGenesToGoReport Man page
annot2Color Man page Source code
annot2col Man page
annot2col,MineICAParams-method Man page
annot2col<- Man page
annot2col<-,MineICAParams,character-method Man page
annot2col<-,MineICAParams-method Man page
annotCarbayo Man page
annotFeatures Man page Source code
annotFeaturesComp Man page Source code
annotFeaturesWithBiomaRt Man page Source code
annotInGene Man page Source code
annotReciprocal Man page Source code
annotfile Man page
annotfile,MineICAParams-method Man page
annotfile<- Man page
annotfile<-,MineICAParams,character-method Man page
annotfile<-,MineICAParams-method Man page
buildIcaSet Man page Source code
buildMineICAParams Man page Source code
build_sortHeatmap Man page Source code
calcCoord Source code
chipManu Man page
chipManu,IcaSet-method Man page
chipManu<- Man page
chipManu<-,IcaSet,character-method Man page
chipManu<-,IcaSet-method Man page
chipVersion Man page
chipVersion,IcaSet-method Man page
chipVersion<- Man page
chipVersion<-,IcaSet,character-method Man page
chipVersion<-,IcaSet-method Man page
clScore Source code
class:IcaSet Man page
class:MineICAParams Man page
clusVarAnalysis Man page Source code
clusterFastICARuns Man page Source code
clusterSamplesByComp Man page Source code
clusterSamplesByComp_multiple Man page Source code
compNames Man page Man page
compNames,IcaSet-method Man page
compNames<- Man page Man page
compNames<-,IcaSet,character-method Man page
compNames<-,IcaSet-method Man page
compareAn Man page Source code
compareAn2graphfile Man page Source code
compareGenes Man page Source code
cor2An Man page Source code
correl2Comp Man page Source code
cutoff.biMod Source code
dat Man page Man page
dat,IcaSet-method Man page Man page
dat<- Man page Man page
dat<-,IcaSet,matrix-method Man page Man page
dat<-,IcaSet-method Man page
datByGene Man page
datByGene,IcaSet-method Man page
datByGene<- Man page
datByGene<-,IcaSet,matrix-method Man page
datByGene<-,IcaSet-method Man page
dataCarbayo Man page
datfile Man page
datfile,MineICAParams-method Man page
datfile<- Man page
datfile<-,MineICAParams,character-method Man page
datfile<-,MineICAParams-method Man page
doEnrichment Man page Source code
geneNames Man page
geneNames,IcaSet-method Man page
genesPath Man page
genesPath,MineICAParams-method Man page
genesPath<- Man page
genesPath<-,ANY-method Man page
genesPath<-,MineICAParams,character-method Man page
getA Man page
getA,IcaSet-method Man page
getAfile Man page
getAnnot2col Man page
getAnnotfile Man page
getChipManu,IcaSet-method Man page
getComp Man page
getComp,IcaSet,character,numeric Man page
getComp,IcaSet,character,numeric-method Man page
getComp,IcaSet-method Man page
getGenesPath Man page
getIndComp Man page
getIndComp,IcaSet-method Man page
getLabelsComp Man page
getLabelsComp,IcaSet-method Man page
getMart,IcaSet-method Man page
getProj Man page Source code
getPvalCutoff Man page
getRefSamples,IcaSet-method Man page
getResPath Man page
getS Man page
getS,IcaSet-method Man page
getSByGene Man page
getSByGene,IcaSet-method Man page
getSdExpr Man page Source code
getSelCutoff Man page
getSfile Man page
getTypeID,IcaSet-method Man page
getWitGenes Man page
getWitGenes,IcaSet-method Man page
getdatfile Man page
heatmap.plus Source code
hgOver Man page
hypergeoAn Man page Source code
icaSetCarbayo Man page
icaSetKim Man page
icaSetRiester Man page
icaSetStransky Man page
indComp Man page Man page
indComp,IcaSet-method Man page
indComp<- Man page Man page
indComp<-,IcaSet,character-method Man page
indComp<-,IcaSet-method Man page
mart Man page
mart,IcaSet-method Man page
mart<- Man page
mart<-,IcaSet,character-method Man page
mart<-,IcaSet-method Man page
mergeGostatsResults Man page Source code
nbComp Man page
nbComp,IcaSet-method Man page
nbOccByGeneInComp Man page Source code
nbOccInComp Man page Source code
nbOccInComp_simple Man page Source code
nodeAttrs Man page Source code
organism Man page
organism,IcaSet-method Man page
organism<- Man page
organism<-,IcaSet-method Man page
plotAllMix Man page Source code
plotCorGraph Man page Source code
plotDens2classInComp_plotOnly Man page Source code
plotDensAllAnnotInAllComp Man page Source code
plotDensOneAnnotInAllComp Man page Source code
plotMclust Man page Source code
plotMix Man page Source code
plotNumVarComp Source code
plotPos2classInComp Source code
plotPosAnnotInComp Man page Source code
plotPosOneAnnotInComp_ggplot Man page Source code
plotPosOneAnnotLevInComp_ggplot Man page Source code
plotPosSamplesInComp Man page Source code
plotPosSamplesInComp_ggplot Source code
plot_heatmapsOnSel Man page Source code
pvalCutoff Man page
pvalCutoff,MineICAParams-method Man page
pvalCutoff<- Man page
pvalCutoff<-,MineICAParams,numeric-method Man page
pvalCutoff<-,MineICAParams-method Man page
qualVarAnalysis Man page Source code
quantVarAnalysis Man page Source code
readA Man page Source code
readS Man page Source code
refSamples Man page
refSamples,IcaSet-method Man page
refSamples<- Man page
refSamples<-,IcaSet,character-method Man page
refSamples<-,IcaSet-method Man page
relativePath Man page Source code
resPath Man page
resPath,MineICAParams-method Man page
resPath<- Man page
resPath<-,ANY-method Man page
resPath<-,MineICAParams,character-method Man page
runAn Man page Source code
runCompareIcaSets Man page Source code
runEnrich Man page Source code
runICA Man page Source code
sampleNames<- Man page
sampleNames<-,IcaSet-method Man page
selCutoff Man page
selCutoff,MineICAParams-method Man page
selCutoff<- Man page
selCutoff<-,MineICAParams,numeric-method Man page
selCutoff<-,MineICAParams-method Man page
selectContrib Man page
selectContrib,IcaSet,numeric,character-method Man page
selectContrib,IcaSet-method Man page
selectContrib,list,numeric,ANY Man page
selectContrib,list,numeric,ANY-method Man page
selectFeatures_IQR Man page Source code
selectWitnessGenes Man page Source code
setA,IcaSet-method Man page
setA<- Man page
setAfile Man page
setAnnot2col Man page
setAnnotfile Man page
setChipManu,IcaSet-method Man page
setGenesPath Man page
setIndComp Man page
setIndComp,IcaSet-method Man page
setLabelsComp Man page
setLabelsComp,IcaSet-method Man page
setMart,IcaSet-method Man page
setPvalCutoff Man page
setRefSamples,IcaSet-method Man page
setResPath Man page
setS,IcaSet-method Man page
setS<- Man page
setSByGene,IcaSet-method Man page
setSByGene<- Man page
setSelCutoff Man page
setSfile Man page
setTypeID,IcaSet-method Man page
setWitGenes Man page
setWitGenes,IcaSet-method Man page
setdatfile Man page
subIcaSet Source code
typeID Man page
typeID,IcaSet-method Man page
typeID<- Man page
typeID<-,IcaSet,list-method Man page
typeID<-,IcaSet-method Man page
validIcaSet Source code
wilcoxOrKruskalOnA Man page Source code
witGenes Man page Man page
witGenes,IcaSet-method Man page
witGenes<- Man page Man page
witGenes<-,IcaSet,character-method Man page
witGenes<-,IcaSet-method Man page
writeGenes Man page Source code
writeGostatsHtmltable Man page Source code
writeHtmlResTestsByAnnot Man page Source code
writeProjByComp Man page Source code
writeRnkFiles Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGeneric.R
R/compareAnalysis.R
R/compareGenes.R
R/functions.R
R/functions_comp2annot.R
R/functions_comp2annottests.R
R/functions_enrich.R
R/heatmap.plus.R
R/heatmapsOnSel.R
R/methods-IcaSet.R
R/methods-MineICAParams.R
R/runAn.R
build
build/vignette.rds
data
data/icaSetCarbayo.rda
inst
inst/doc
inst/doc/MineICA.R
inst/doc/MineICA.Rnw
inst/doc/MineICA.pdf
man
man/A.Rd
man/Alist.Rd
man/Slist.Rd
man/addGenesToGoReport.Rd
man/annot2Color.Rd
man/annotCarbayo.Rd
man/annotFeatures.Rd
man/annotFeaturesComp.Rd
man/annotFeaturesWithBiomaRt.Rd
man/annotInGene.Rd
man/annotReciprocal.Rd
man/buildIcaSet.Rd
man/buildMineICAParams.Rd
man/build_sortHeatmap.Rd
man/class-IcaSet.Rd
man/class-MineICAParams.Rd
man/clusVarAnalysis.Rd
man/clusterFastICARuns.Rd
man/clusterSamplesByComp.Rd
man/clusterSamplesByComp_multiple.Rd
man/compareAn.Rd
man/compareAn2graphfile.Rd
man/compareGenes.Rd
man/cor2An.Rd
man/correl2Comp.Rd
man/dat.Rd
man/dataCarbayo.Rd
man/doEnrichment.Rd
man/getComp.Rd
man/getProj.Rd
man/getSdExpr.Rd
man/hgOver.Rd
man/hypergeoAn.Rd
man/icaSetCarbayo.Rd
man/icaSetKim.Rd
man/icaSetRiester.Rd
man/icaSetStransky.Rd
man/indComp.Rd
man/mergeGostatsResults.Rd
man/nbOccByGeneInComp.Rd
man/nbOccInComp.Rd
man/nbOccInComp_simple.Rd
man/nodeAttrs.Rd
man/plotAllMix.Rd
man/plotCorGraph.Rd
man/plotDens2classInComp_plotOnly.Rd
man/plotDensAllAnnotInAllComp.Rd
man/plotDensOneAnnotInAllComp.Rd
man/plotMclust.Rd
man/plotMix.Rd
man/plotPosAnnotInComp.Rd
man/plotPosOneAnnotInComp_ggplot.Rd
man/plotPosOneAnnotLevInComp_ggplot.Rd
man/plotPosSamplesInComp.Rd
man/plot_heatmapsOnSel.Rd
man/qualVarAnalysis.Rd
man/quantVarAnalysis.Rd
man/readA.Rd
man/readS.Rd
man/relativePath.Rd
man/runAn.Rd
man/runCompareIcaSets.Rd
man/runEnrich.Rd
man/runICA.Rd
man/selectContrib.Rd
man/selectFeatures_IQR.Rd
man/selectWitnessGenes.Rd
man/wilcoxOrKruskalOnA.Rd
man/writeGenes.Rd
man/writeGostatsHtmltable.Rd
man/writeHtmlResTestsByAnnot.Rd
man/writeProjByComp.Rd
man/writeRnkFiles.Rd
vignettes
vignettes/MineICA.Rnw
vignettes/bibli.bib
vignettes/images
vignettes/images/2_orderedByContrib_zval3.pdf
vignettes/images/2_withDendro_zval3.pdf
vignettes/images/erhist.png
vignettes/images/graphBreast.jpg
MineICA documentation built on May 20, 2017, 10:29 p.m.