MineICA: Analysis of an ICA decomposition obtained on genomics data

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.

AuthorAnne Biton
Date of publicationNone
MaintainerAnne Biton <anne.biton@gmail.com>
LicenseGPL-2
Version1.14.0

View on Bioconductor

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

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

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

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