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.
|Date of publication||None|
|Maintainer||Anne Biton <email@example.com>|
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.
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
compareGenes: Union and intersection of contributing genes
cor2An: Correlation between two matrices
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
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...
nbOccInComp: Select components the features contribute to
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
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
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...
writeRnkFiles: Write rnk files containing gene projections