API for MineICA
Analysis of an ICA decomposition obtained on genomics data

Global 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
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`	Source code
addGenesToGoReport	Man page
annot2Color	Man page
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
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
build_sortHeatmap	Man page
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-MineICAParams	Man page
class:IcaSet	Man page
class:MineICAParams	Man page
clusVarAnalysis	Man page
clusterFastICARuns	Man page Source code
clusterSamplesByComp	Man page
clusterSamplesByComp_multiple	Man page
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
compareAn2graphfile	Man page
compareGenes	Man page Source code
cor2An	Man page
correl2Comp	Man page
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
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
getSelCutoff	Man page
getSfile	Man page
getTypeID,IcaSet-method	Man page
getWitGenes	Man page
getWitGenes,IcaSet-method	Man page
getdatfile	Man page
hgOver	Man page
hypergeoAn	Man page
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
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
plotCorGraph	Man page Source code
plotDens2classInComp_plotOnly	Man page
plotDensAllAnnotInAllComp	Man page
plotDensOneAnnotInAllComp	Man page
plotMclust	Man page
plotMix	Man page
plotPosAnnotInComp	Man page Source code
plotPosOneAnnotInComp_ggplot	Man page Source code
plotPosOneAnnotLevInComp_ggplot	Man page Source code
plotPosSamplesInComp	Man page
plotPosSamplesInComp_ggplot	Source code
plot_heatmapsOnSel	Man page
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
readS	Man page
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
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
writeGostatsHtmltable	Man page Source code
writeHtmlResTestsByAnnot	Man page Source code
writeProjByComp	Man page Source code
writeRnkFiles	Man page Source code