MineICA: Analysis of an ICA decomposition obtained on genomics data

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.

AuthorAnne Biton
Date of publicationNone
MaintainerAnne Biton <anne.biton@gmail.com>
LicenseGPL-2
Version1.14.0

View on Bioconductor

Man pages

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

addGenesToGoReport: Add Symbol IDs to hyperGTest results

Alist: Retrieve sample contributions stored in an 'IcaSet' object as...

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

build_sortHeatmap: Build the heatmap matrices

class-IcaSet: Class to Contain and Describe an ICA decomposition of...

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

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

cor2An: Correlation between two matrices

correl2Comp: correl2Comp

dat: Retrieve and set data from IcaSet

dataCarbayo: Carbayo expression data

doEnrichment: Runs enrichment analysis of contributing genes

getComp: Retrieve feature and sample values on a component stored in...

getProj: Extract projection values

getSdExpr: getSdExpr

hgOver: Output of 'hyperGtest'

hypergeoAn: Runs an enrichment analysis per component using package...

icaSetCarbayo: IcaSet-object containing a FastICA decomposition of gene...

icaSetKim: IcaSet-object containing a FastICA decomposition of gene...

icaSetRiester: IcaSet-object containing a FastICA decomposition of gene...

icaSetStransky: IcaSet-object containing a FastICA decomposition of gene...

indComp: Retrieve and set component labels, indices, and witness genes...

mergeGostatsResults: Merge enrichment results obtained for different databases...

nbOccByGeneInComp: nbOccByGeneInComp

nbOccInComp: Select components the features contribute to

nbOccInComp_simple: nbOccInComp_simple

nodeAttrs: Generate node attributes

plotAllMix: Plots the Gaussian fitted by 'Mclust' on several numeric...

plotCorGraph: Plots graph using

plotDens2classInComp_plotOnly: Plots the densities or boxplots of the component...

plotDensAllAnnotInAllComp: Tests if groups of samples are differently distributed on the...

plotDensOneAnnotInAllComp: Tests if groups of samples are differently distributed on the...

plot_heatmapsOnSel: Plot heatmap associated with each component

plotMclust: Plots the Gaussian fitted by 'Mclust'

plotMix: Plots an histogram and Gaussian fitted by 'Mclust'

plotPosAnnotInComp: Histograms of sample contributions for each annotation level

plotPosOneAnnotInComp_ggplot: Tests if groups of samples are differently distributed on the...

plotPosOneAnnotLevInComp_ggplot: Plots the position of a subset of samples in the histogram of...

plotPosSamplesInComp: Histograms of sample subsets

qualVarAnalysis: Tests association between qualitative variables and...

quantVarAnalysis: Correlation between variables and components.

readA: read A

readS: read S

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

Slist: Retrieve feature/gene projections stored in an 'IcaSet'...

wilcoxOrKruskalOnA: Comparison of distributions of sample groups

writeGenes: Description of features using package 'biomaRt'.

writeGostatsHtmltable: Writes enrichment results in a HTML file

writeHtmlResTestsByAnnot: Tests if groups of samples are differently distributed on the...

writeProjByComp: writeProjByComp

writeRnkFiles: Write rnk files containing gene projections

Files in this package

MineICA/DESCRIPTION
MineICA/NAMESPACE
MineICA/R
MineICA/R/AllClasses.R MineICA/R/AllGeneric.R MineICA/R/compareAnalysis.R MineICA/R/compareGenes.R MineICA/R/functions.R MineICA/R/functions_comp2annot.R MineICA/R/functions_comp2annottests.R MineICA/R/functions_enrich.R MineICA/R/heatmap.plus.R MineICA/R/heatmapsOnSel.R MineICA/R/methods-IcaSet.R MineICA/R/methods-MineICAParams.R MineICA/R/runAn.R
MineICA/build
MineICA/build/vignette.rds
MineICA/data
MineICA/data/icaSetCarbayo.rda
MineICA/inst
MineICA/inst/doc
MineICA/inst/doc/MineICA.R
MineICA/inst/doc/MineICA.Rnw
MineICA/inst/doc/MineICA.pdf
MineICA/man
MineICA/man/A.Rd MineICA/man/Alist.Rd MineICA/man/Slist.Rd MineICA/man/addGenesToGoReport.Rd MineICA/man/annot2Color.Rd MineICA/man/annotCarbayo.Rd MineICA/man/annotFeatures.Rd MineICA/man/annotFeaturesComp.Rd MineICA/man/annotFeaturesWithBiomaRt.Rd MineICA/man/annotInGene.Rd MineICA/man/annotReciprocal.Rd MineICA/man/buildIcaSet.Rd MineICA/man/buildMineICAParams.Rd MineICA/man/build_sortHeatmap.Rd MineICA/man/class-IcaSet.Rd MineICA/man/class-MineICAParams.Rd MineICA/man/clusVarAnalysis.Rd MineICA/man/clusterFastICARuns.Rd MineICA/man/clusterSamplesByComp.Rd MineICA/man/clusterSamplesByComp_multiple.Rd MineICA/man/compareAn.Rd MineICA/man/compareAn2graphfile.Rd MineICA/man/compareGenes.Rd MineICA/man/cor2An.Rd MineICA/man/correl2Comp.Rd MineICA/man/dat.Rd MineICA/man/dataCarbayo.Rd MineICA/man/doEnrichment.Rd MineICA/man/getComp.Rd MineICA/man/getProj.Rd MineICA/man/getSdExpr.Rd MineICA/man/hgOver.Rd MineICA/man/hypergeoAn.Rd MineICA/man/icaSetCarbayo.Rd MineICA/man/icaSetKim.Rd MineICA/man/icaSetRiester.Rd MineICA/man/icaSetStransky.Rd MineICA/man/indComp.Rd MineICA/man/mergeGostatsResults.Rd MineICA/man/nbOccByGeneInComp.Rd MineICA/man/nbOccInComp.Rd MineICA/man/nbOccInComp_simple.Rd MineICA/man/nodeAttrs.Rd MineICA/man/plotAllMix.Rd MineICA/man/plotCorGraph.Rd MineICA/man/plotDens2classInComp_plotOnly.Rd MineICA/man/plotDensAllAnnotInAllComp.Rd MineICA/man/plotDensOneAnnotInAllComp.Rd MineICA/man/plotMclust.Rd MineICA/man/plotMix.Rd MineICA/man/plotPosAnnotInComp.Rd MineICA/man/plotPosOneAnnotInComp_ggplot.Rd MineICA/man/plotPosOneAnnotLevInComp_ggplot.Rd MineICA/man/plotPosSamplesInComp.Rd MineICA/man/plot_heatmapsOnSel.Rd MineICA/man/qualVarAnalysis.Rd MineICA/man/quantVarAnalysis.Rd MineICA/man/readA.Rd MineICA/man/readS.Rd MineICA/man/relativePath.Rd MineICA/man/runAn.Rd MineICA/man/runCompareIcaSets.Rd MineICA/man/runEnrich.Rd MineICA/man/runICA.Rd MineICA/man/selectContrib.Rd MineICA/man/selectFeatures_IQR.Rd MineICA/man/selectWitnessGenes.Rd MineICA/man/wilcoxOrKruskalOnA.Rd MineICA/man/writeGenes.Rd MineICA/man/writeGostatsHtmltable.Rd MineICA/man/writeHtmlResTestsByAnnot.Rd MineICA/man/writeProjByComp.Rd MineICA/man/writeRnkFiles.Rd
MineICA/vignettes
MineICA/vignettes/MineICA.Rnw
MineICA/vignettes/bibli.bib
MineICA/vignettes/images
MineICA/vignettes/images/2_orderedByContrib_zval3.pdf
MineICA/vignettes/images/2_withDendro_zval3.pdf
MineICA/vignettes/images/erhist.png
MineICA/vignettes/images/graphBreast.jpg

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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