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