Analysis of an ICA decomposition obtained on genomics data

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Documentation for package ‘MineICA’ version 1.42.0

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

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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-MineICAParams	Class to contain parameters for the analysis of an ICA decomposition.
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.
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.

-- 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.
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.