A                       Retrieve and set Source S and Mixing matrix A
                        from IcaSet
Alist                   Retrieve sample contributions stored in an
                        'IcaSet' object as a list.
IcaSet                  Class to Contain and Describe an ICA
                        decomposition of High-Throughput Data.
MineICAParams           Class to contain parameters for the analysis of
                        an ICA decomposition.
Slist                   Retrieve feature/gene projections stored in an
                        'IcaSet' object as a list.
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
clusVarAnalysis         Tests association between clusters of samples
                        and variables
clusterFastICARuns      Run of fastICA and JADE algorithms
clusterSamplesByComp    Cluster samples from an IcaSet
clusterSamplesByComp_multiple
                        Cluster samples from an IcaSet
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
getComp                 Retrieve feature and sample values on a
                        component stored in an 'IcaSet' object.
getProj                 Extract projection values
hgOver                  Output of 'hyperGtest'
hypergeoAn              Runs an enrichment analysis per component using
                        package 'GOstats'.
icaSetCarbayo           IcaSet-object containing a FastICA
                        decomposition of gene expression
                        microarrray-based data of bladder cancer
                        samples.
icaSetKim               IcaSet-object containing a FastICA
                        decomposition of gene expression
                        microarrray-based data of bladder cancer
                        samples.
icaSetRiester           IcaSet-object containing a FastICA
                        decomposition of gene expression
                        microarrray-based data of bladder cancer
                        samples.
icaSetStransky          IcaSet-object containing a FastICA
                        decomposition of gene expression
                        microarrray-based data of bladder cancer
                        samples.
indComp                 Retrieve and set component labels, indices, and
                        witness genes from IcaSet
nbOccByGeneInComp       nbOccByGeneInComp
nbOccInComp             Select components the features contribute to
nodeAttrs               Generate node attributes
plotAllMix              Plots the Gaussian fitted by 'Mclust' on
                        several numeric vectors
plotCorGraph            Plots graph using
plotMix                 Plots an histogram and Gaussian fitted by
                        'Mclust'
plotPosAnnotInComp      Histograms of sample contributions for each
                        annotation level
plot_heatmapsOnSel      Plot heatmap associated with each component
qualVarAnalysis         Tests association between qualitative variables
                        and components.
quantVarAnalysis        Correlation between variables and components.
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
writeGenes              Description of features using package
                        'biomaRt'.
writeProjByComp         writeProjByComp
writeRnkFiles           Write rnk files containing gene projections
