Man pages for MineICA
Analysis of an ICA decomposition obtained on genomics data

ARetrieve and set Source S and Mixing matrix A from IcaSet
addGenesToGoReportAdd Symbol IDs to hyperGTest results
AlistRetrieve sample contributions stored in an 'IcaSet' object as...
annot2ColorAssociation of a colour with each annotation level
annotCarbayoCarbayo annotation data
annotFeaturesAnnotation of features using an annotation package
annotFeaturesCompFeatures annotation
annotFeaturesWithBiomaRtAnnotation of features using 'biomaRt'
annotInGeneFeatures annotation of an object of class IcaSet.
buildIcaSetThis function builds an object of class 'IcaSet'.
buildMineICAParamsCreates an object of class MineICAParams
build_sortHeatmapBuild the heatmap matrices
class-IcaSetClass to Contain and Describe an ICA decomposition of...
class-MineICAParamsClass to contain parameters for the analysis of an ICA...
clusterFastICARunsRun of fastICA and JADE algorithms
clusterSamplesByCompCluster samples from an IcaSet
clusterSamplesByComp_multipleCluster samples from an IcaSet
clusVarAnalysisTests association between clusters of samples and variables
compareAnComparison of IcaSet objects using correlation
compareGenesUnion and intersection of contributing genes
cor2AnCorrelation between two matrices
datRetrieve and set data from IcaSet
dataCarbayoCarbayo expression data
doEnrichmentRuns enrichment analysis of contributing genes
getCompRetrieve feature and sample values on a component stored in...
getProjExtract projection values
hgOverOutput of 'hyperGtest'
hypergeoAnRuns an enrichment analysis per component using package...
icaSetCarbayoIcaSet-object containing a FastICA decomposition of gene...
icaSetKimIcaSet-object containing a FastICA decomposition of gene...
icaSetRiesterIcaSet-object containing a FastICA decomposition of gene...
icaSetStranskyIcaSet-object containing a FastICA decomposition of gene...
indCompRetrieve and set component labels, indices, and witness genes...
mergeGostatsResultsMerge enrichment results obtained for different databases...
nbOccInCompSelect components the features contribute to
nodeAttrsGenerate node attributes
plotAllMixPlots the Gaussian fitted by 'Mclust' on several numeric...
plotCorGraphPlots graph using
plotDens2classInComp_plotOnlyPlots the densities or boxplots of the component...
plotDensAllAnnotInAllCompTests if groups of samples are differently distributed on the...
plotDensOneAnnotInAllCompTests if groups of samples are differently distributed on the...
plot_heatmapsOnSelPlot heatmap associated with each component
plotMclustPlots the Gaussian fitted by 'Mclust'
plotMixPlots an histogram and Gaussian fitted by 'Mclust'
plotPosAnnotInCompHistograms of sample contributions for each annotation level
plotPosOneAnnotInComp_ggplotTests if groups of samples are differently distributed on the...
plotPosOneAnnotLevInComp_ggplotPlots the position of a subset of samples in the histogram of...
plotPosSamplesInCompHistograms of sample subsets
qualVarAnalysisTests association between qualitative variables and...
quantVarAnalysisCorrelation between variables and components.
readAread A
readSread S
relativePathRelative path
runAnRun analysis of an IcaSet object
runEnrichEnrichment analysis through GOstats
runICARun of fastICA and JADE algorithms
selectContribSelect contributing features/genes
selectFeatures_IQRSelection of features based on their IQR
SlistRetrieve feature/gene projections stored in an 'IcaSet'...
wilcoxOrKruskalOnAComparison of distributions of sample groups
writeGenesDescription of features using package 'biomaRt'.
writeGostatsHtmltableWrites enrichment results in a HTML file
writeHtmlResTestsByAnnotTests if groups of samples are differently distributed on the...
writeRnkFilesWrite rnk files containing gene projections
MineICA documentation built on Nov. 8, 2020, 5:35 p.m.