# Analysis of an ICA decomposition obtained on genomics data

## Documentation for package ‘MineICA’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D G H I M N O P Q R S T W misc

## -- A --

A | Retrieve and set Source S and Mixing matrix A from IcaSet
A-method | Retrieve and set Source S and Mixing matrix A from IcaSet
A<- | Retrieve and set Source S and Mixing matrix A from IcaSet
A<--method | Retrieve and set Source S and Mixing matrix A from IcaSet
Afile | Class to contain parameters for the analysis of an ICA decomposition.
Afile-method | Class to contain parameters for the analysis of an ICA decomposition.
Afile<- | Class to contain parameters for the analysis of an ICA decomposition.
Afile<--method | Class to contain parameters for the analysis of an ICA decomposition.
Alist | Retrieve sample contributions stored in an 'IcaSet' object as a list.
Alist-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
annot2col | Class to contain parameters for the analysis of an ICA decomposition.
annot2col-method | Class to contain parameters for the analysis of an ICA decomposition.
annot2col<- | Class to contain parameters for the analysis of an ICA decomposition.
annot2col<--method | Class to contain parameters for the analysis of an ICA decomposition.
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'
annotfile | Class to contain parameters for the analysis of an ICA decomposition.
annotfile-method | Class to contain parameters for the analysis of an ICA decomposition.
annotfile<- | Class to contain parameters for the analysis of an ICA decomposition.
annotfile<--method | Class to contain parameters for the analysis of an ICA decomposition.
annotInGene | Features annotation of an object of class IcaSet.
annotReciprocal | annotReciprocal

## -- B --

buildIcaSet | This function builds an object of class 'IcaSet'.
buildMineICAParams | Creates an object of class MineICAParams

## -- C --

chipManu | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
chipManu-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
chipManu<- | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
chipManu<--method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
chipVersion | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
chipVersion-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
chipVersion<- | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
chipVersion<--method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
class:IcaSet | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
class:MineICAParams | Class to contain parameters for the analysis of an ICA decomposition.
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
compNames | Retrieve and set component labels, indices, and witness genes from IcaSet
compNames-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
compNames<- | Retrieve and set component labels, indices, and witness genes from IcaSet
compNames<--method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
compNames<--method | Retrieve and set component labels, indices, and witness genes from IcaSet
cor2An | Correlation between two matrices
correl2Comp | correl2Comp

## -- D --

dat | Retrieve and set data from IcaSet
dat-method | Retrieve and set data from IcaSet
dat<- | Retrieve and set data from IcaSet
dat<--method | Retrieve and set data from IcaSet
dataCarbayo | Carbayo expression data
datByGene | Retrieve and set data from IcaSet
datByGene-method | Retrieve and set data from IcaSet
datByGene<- | Retrieve and set data from IcaSet
datByGene<--method | Retrieve and set data from IcaSet
datfile | Class to contain parameters for the analysis of an ICA decomposition.
datfile-method | Class to contain parameters for the analysis of an ICA decomposition.
datfile<- | Class to contain parameters for the analysis of an ICA decomposition.
datfile<--method | Class to contain parameters for the analysis of an ICA decomposition.

## -- G --

geneNames | Retrieve and set data from IcaSet
geneNames-method | Retrieve and set data from IcaSet
genesPath | Class to contain parameters for the analysis of an ICA decomposition.
genesPath-method | Class to contain parameters for the analysis of an ICA decomposition.
genesPath<- | Class to contain parameters for the analysis of an ICA decomposition.
genesPath<--method | Class to contain parameters for the analysis of an ICA decomposition.
getA | Retrieve and set Source S and Mixing matrix A from IcaSet
getA-method | Retrieve and set Source S and Mixing matrix A from IcaSet
getAfile | Class to contain parameters for the analysis of an ICA decomposition.
getAnnot2col | Class to contain parameters for the analysis of an ICA decomposition.
getAnnotfile | Class to contain parameters for the analysis of an ICA decomposition.
getChipManu-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
getComp | Retrieve feature and sample values on a component stored in an 'IcaSet' object.
getComp,IcaSet,character,numeric | Retrieve feature and sample values on a component stored in an 'IcaSet' object.
getComp-method | Retrieve feature and sample values on a component stored in an 'IcaSet' object.
getdatfile | Class to contain parameters for the analysis of an ICA decomposition.
getGenesPath | Class to contain parameters for the analysis of an ICA decomposition.
getIndComp | Retrieve and set component labels, indices, and witness genes from IcaSet
getIndComp-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
getLabelsComp | Retrieve and set component labels, indices, and witness genes from IcaSet
getLabelsComp-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
getMart-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
getOrganism-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
getProj | Extract projection values
getPvalCutoff | Class to contain parameters for the analysis of an ICA decomposition.
getRefSamples-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
getResPath | Class to contain parameters for the analysis of an ICA decomposition.
getS | Retrieve and set Source S and Mixing matrix A from IcaSet
getS-method | Retrieve and set Source S and Mixing matrix A from IcaSet
getSByGene | Retrieve and set Source S and Mixing matrix A from IcaSet
getSByGene-method | Retrieve and set Source S and Mixing matrix A from IcaSet
getSelCutoff | Class to contain parameters for the analysis of an ICA decomposition.
getSfile | Class to contain parameters for the analysis of an ICA decomposition.
getTypeID-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
getWitGenes | Retrieve and set component labels, indices, and witness genes from IcaSet

## -- H --

hgOver | Output of 'hyperGtest'
hypergeoAn | Runs an enrichment analysis per component using package 'GOstats'.

## -- I --

IcaSet | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
IcaSet-class | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
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
indComp-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
indComp<- | Retrieve and set component labels, indices, and witness genes from IcaSet
indComp<--method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
indComp<--method | Retrieve and set component labels, indices, and witness genes from IcaSet

## -- M --

mart | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
mart-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
mart<- | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
mart<--method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
MineICAParams | Class to contain parameters for the analysis of an ICA decomposition.
MineICAParams-class | Class to contain parameters for the analysis of an ICA decomposition.

## -- N --

nbComp | Retrieve and set Source S and Mixing matrix A from IcaSet
nbComp-method | Retrieve and set Source S and Mixing matrix A from IcaSet
nbOccByGeneInComp | nbOccByGeneInComp
nbOccInComp | Select components the features contribute to
nodeAttrs | Generate node attributes

## -- O --

organism | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
organism-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
organism<- | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
organism<--method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.

## -- P --

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
pvalCutoff | Class to contain parameters for the analysis of an ICA decomposition.
pvalCutoff-method | Class to contain parameters for the analysis of an ICA decomposition.
pvalCutoff<- | Class to contain parameters for the analysis of an ICA decomposition.
pvalCutoff<--method | Class to contain parameters for the analysis of an ICA decomposition.

## -- Q --

qualVarAnalysis | Tests association between qualitative variables and components.
quantVarAnalysis | Correlation between variables and components.

## -- R --

refSamples | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
refSamples-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
refSamples<- | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
refSamples<--method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
relativePath | Relative path
resPath | Class to contain parameters for the analysis of an ICA decomposition.
resPath-method | Class to contain parameters for the analysis of an ICA decomposition.
resPath<- | Class to contain parameters for the analysis of an ICA decomposition.
resPath<--method | Class to contain parameters for the analysis of an ICA decomposition.
runAn | Run analysis of an IcaSet object
runCompareIcaSets | runCompareIcaSets
runEnrich | Enrichment analysis through GOstats
runICA | Run of fastICA and JADE algorithms

## -- S --

S | Retrieve and set Source S and Mixing matrix A from IcaSet
S-method | Retrieve and set Source S and Mixing matrix A from IcaSet
S<- | Retrieve and set Source S and Mixing matrix A from IcaSet
S<--method | Retrieve and set Source S and Mixing matrix A from IcaSet
SByGene | Retrieve and set Source S and Mixing matrix A from IcaSet
SByGene-method | Retrieve and set Source S and Mixing matrix A from IcaSet
SByGene<- | Retrieve and set Source S and Mixing matrix A from IcaSet
SByGene<--method | Retrieve and set Source S and Mixing matrix A from IcaSet
selCutoff | Class to contain parameters for the analysis of an ICA decomposition.
selCutoff-method | Class to contain parameters for the analysis of an ICA decomposition.
selCutoff<- | Class to contain parameters for the analysis of an ICA decomposition.
selCutoff<--method | Class to contain parameters for the analysis of an ICA decomposition.
selectContrib | Select contributing features/genes
selectContrib,list,numeric,ANY | Select contributing features/genes
selectContrib-method | Select contributing features/genes
selectFeatures_IQR | Selection of features based on their IQR
selectWitnessGenes | selectWitnessGenes
setA-method | Retrieve and set Source S and Mixing matrix A from IcaSet
setA<- | Retrieve and set Source S and Mixing matrix A from IcaSet
setAfile | Class to contain parameters for the analysis of an ICA decomposition.
setAnnot2col | Class to contain parameters for the analysis of an ICA decomposition.
setAnnotfile | Class to contain parameters for the analysis of an ICA decomposition.
setChipManu-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
setdatfile | Class to contain parameters for the analysis of an ICA decomposition.
setGenesPath | Class to contain parameters for the analysis of an ICA decomposition.
setIndComp | Retrieve and set component labels, indices, and witness genes from IcaSet
setIndComp-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
setLabelsComp | Retrieve and set component labels, indices, and witness genes from IcaSet
setLabelsComp-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
setMart-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
setOrganism-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
setPvalCutoff | Class to contain parameters for the analysis of an ICA decomposition.
setRefSamples-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
setResPath | Class to contain parameters for the analysis of an ICA decomposition.
setS-method | Retrieve and set Source S and Mixing matrix A from IcaSet
setS<- | Retrieve and set Source S and Mixing matrix A from IcaSet
setSByGene-method | Retrieve and set Source S and Mixing matrix A from IcaSet
setSByGene<- | Retrieve and set Source S and Mixing matrix A from IcaSet
setSelCutoff | Class to contain parameters for the analysis of an ICA decomposition.
setSfile | Class to contain parameters for the analysis of an ICA decomposition.
setTypeID-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
setWitGenes | Retrieve and set component labels, indices, and witness genes from IcaSet
Sfile | Class to contain parameters for the analysis of an ICA decomposition.
Sfile-method | Class to contain parameters for the analysis of an ICA decomposition.
Sfile<- | Class to contain parameters for the analysis of an ICA decomposition.
Sfile<--method | Class to contain parameters for the analysis of an ICA decomposition.
Slist | Retrieve feature/gene projections stored in an 'IcaSet' object as a list.
Slist-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
SlistByGene | Retrieve feature/gene projections stored in an 'IcaSet' object as a list.
SlistByGene-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.

## -- T --

typeID | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
typeID-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
typeID<- | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
typeID<--method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.

## -- W --

witGenes | Retrieve and set component labels, indices, and witness genes from IcaSet
witGenes-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
witGenes<- | Retrieve and set component labels, indices, and witness genes from IcaSet
witGenes<--method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
witGenes<--method | Retrieve and set component labels, indices, and witness genes from IcaSet
writeGenes | Description of features using package 'biomaRt'.
writeProjByComp | writeProjByComp
writeRnkFiles | Write rnk files containing gene projections

## -- misc --

[ | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
[-method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
[-method | Class to contain parameters for the analysis of an ICA decomposition.
[<- | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
[<--method | Class to Contain and Describe an ICA decomposition of High-Throughput Data.
[<--method | Class to contain parameters for the analysis of an ICA decomposition.