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.

Author
Anne Biton
Date of publication
None
Maintainer
Anne Biton <anne.biton@gmail.com>
License
GPL-2
Version
1.14.0

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