Analysis of an ICA decomposition obtained on genomics data

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Documentation for package ‘MineICA’ version 1.18.0

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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: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.
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.
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.