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MineICA (version 1.10.0)

Analysis of an ICA decomposition obtained on genomics data

Description

The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.

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Version

Version

1.10.0

License

GPL-2

Maintainer

Anne Biton

Last Published

February 15th, 2017

Functions in MineICA (1.10.0)

annotFeaturesComp

Features annotation
clusterSamplesByComp_multiple

Cluster samples from an IcaSet
annotFeaturesWithBiomaRt

Annotation of features using biomaRt
clusterSamplesByComp

Cluster samples from an IcaSet
getProj

Extract projection values
icaSetCarbayo

IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.
getSdExpr

getSdExpr
icaSetKim

IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.
annotCarbayo

Carbayo annotation data
annotFeatures

Annotation of features using an annotation package
buildMineICAParams

Creates an object of class MineICAParams
IcaSet

Class to Contain and Describe an ICA decomposition of High-Throughput Data.
compareAn2graphfile

compareAn2graphfile
compareGenes

Union and intersection of contributing genes
plotMclust

plotMix

relativePath

Relative path
plotDensAllAnnotInAllComp

Tests if groups of samples are differently distributed on the components according and do the corresponding plots.
plotDensOneAnnotInAllComp

Tests if groups of samples are differently distributed on the components and do the corresponding plots.
Slist

readA

read A
readS

read S
wilcoxOrKruskalOnA

Comparison of distributions of sample groups
runAn

Run analysis of an IcaSet object
runICA

Run of fastICA and JADE algorithms
selectContrib

Select contributing features/genes
Alist

annot2Color

Association of a colour with each annotation level
build_sortHeatmap

Build the heatmap matrices
buildIcaSet

dataCarbayo

Carbayo expression data
dat

Retrieve and set data from IcaSet
annotInGene

Features annotation of an object of class IcaSet.
annotReciprocal

annotReciprocal
hgOver

Output of hyperGtest
hypergeoAn

plotAllMix

Plots the Gaussian fitted by Mclust on several numeric vectors
plot_heatmapsOnSel

Plot heatmap associated with each component
plotPosAnnotInComp

Histograms of sample contributions for each annotation level
plotPosOneAnnotInComp_ggplot

Tests if groups of samples are differently distributed on the components and do the corresponding plots.
MineICAParams

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

Run of fastICA and JADE algorithms
indComp

Retrieve and set component labels, indices, and witness genes from IcaSet
doEnrichment

Runs enrichment analysis of contributing genes
getComp

Retrieve feature and sample values on a component stored in an IcaSet object.
mergeGostatsResults

Merge enrichment results obtained for different databases into one file per component.
selectWitnessGenes

selectWitnessGenes
selectFeatures_IQR

Selection of features based on their IQR
writeHtmlResTestsByAnnot

Tests if groups of samples are differently distributed on the components according and do the corresponding plots.
writeProjByComp

writeProjByComp
A

Retrieve and set Source S and Mixing matrix A from IcaSet
addGenesToGoReport

Add Symbol IDs to hyperGTest results
clusVarAnalysis

Tests association between clusters of samples and variables
compareAn

Comparison of IcaSet objects using correlation
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.
nbOccInComp

Select components the features contribute to
qualVarAnalysis

Tests association between qualitative variables and components.
nodeAttrs

Generate node attributes
quantVarAnalysis

Correlation between variables and components.
writeGenes

Description of features using package biomaRt.
writeGostatsHtmltable

Writes enrichment results in a HTML file
cor2An

Correlation between two matrices
correl2Comp

correl2Comp
nbOccByGeneInComp

nbOccByGeneInComp
nbOccInComp_simple

nbOccInComp_simple
plotCorGraph

Plots graph using
plotDens2classInComp_plotOnly

plotPosSamplesInComp

Histograms of sample subsets
plotPosOneAnnotLevInComp_ggplot

runCompareIcaSets

runCompareIcaSets
runEnrich

writeRnkFiles

Write rnk files containing gene projections