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
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
MineICA documentation built on Nov. 1, 2018, 4:56 a.m.