Package: MineICA 1.45.0
Anne Biton
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.
Authors:
MineICA_1.45.0.tar.gz
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MineICA.pdf |MineICA.html✨
MineICA/json (API)
| # Install 'MineICA' in R: |
| install.packages('MineICA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- icaSetCarbayo - IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.
On BioConductor:MineICA-1.45.0(bioc 3.20)MineICA-1.44.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:678d64f9e3
Exports:AA<-AfileAfile<-Alistannot2colannot2col<-annot2ColorannotFeaturesannotFeaturesCompannotFeaturesWithBiomaRtannotfileannotfile<-annotInGeneannotReciprocalbuildIcaSetbuildMineICAParamschipManuchipManu<-chipVersionchipVersion<-clusterFastICARunsclusterSamplesByCompclusterSamplesByComp_multipleclusVarAnalysiscompareAncompareAn2graphfilecompareGenescompNamescompNames<-cor2Andatdat<-datByGenedatByGene<-datfiledatfile<-geneNamesgenesPathgenesPath<-getCompgetProjgetSdExprhypergeoAnindCompindComp<-martmart<-nbCompnbOccInCompnodeAttrsorganismorganism<-plot_heatmapsOnSelplotAllMixplotCorGraphplotMixplotPosAnnotInCompplotPosSamplesInComppvalCutoffpvalCutoff<-qualVarAnalysisquantVarAnalysisrefSamplesrefSamples<-relativePathresPathresPath<-runAnrunCompareIcaSetsrunEnrichrunICASS<-SByGeneSByGene<-selCutoffselCutoff<-selectContribselectFeatures_IQRselectWitnessGenesSfileSfile<-SlistSlistByGenetypeIDtypeID<-witGeneswitGenes<-writeGeneswriteHtmlResTestsByAnnotwriteProjByCompwriteRnkFiles
Dependencies:abindaffyaffyioannotateAnnotationDbiAnnotationForgeaskpassbackportsbase64base64encbeanplotBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibbumphuntercachemCategorycheckmateclassclicliprclueclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsDEoptimRdigestdiptestdoRNGdplyrevaluatefansifarverfastICAfastmapFDb.InfiniumMethylation.hg19filelockflexmixfontawesomeforeachforeignformatRFormulafpcfsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2glueGO.dbGOstatsgraphgridExtraGSEABasegtablegtoolsHDF5ArrayhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphilluminaioIRangesisobanditeratorsJADEjquerylibjsonliteKEGGRESTkernlabKernSmoothknitrlabelinglambda.rlatticelifecyclelimmalocfitlumilumiHumanAll.dbmagrittrmarrayMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimodeltoolsmulttestmunsellnleqslvnlmennetnor1mixopensslorg.Hs.eg.dbpillarpkgconfigplogrplyrpngprabcluspreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRBGLRColorBrewerRcppRCurlreadrreshapereshape2restfulrRgraphvizrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsrobustbaserpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesscrimesiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Retrieve and set Source S and Mixing matrix A from IcaSet | A A,IcaSet-method A<- A<-,IcaSet,data.frame-method A<-,IcaSet-method getA getA,IcaSet-method getS getS,IcaSet-method getSByGene getSByGene,IcaSet-method nbComp nbComp,IcaSet-method S S,IcaSet-method S<- S<-,IcaSet,data.frame-method S<-,IcaSet-method SByGene SByGene,IcaSet-method SByGene<- SByGene<-,IcaSet,data.frame-method SByGene<-,IcaSet-method setA,IcaSet-method setA<- setS,IcaSet-method setS<- setSByGene,IcaSet-method setSByGene<- |
| Retrieve sample contributions stored in an 'IcaSet' object as a list. | Alist |
| Association of a colour with each annotation level | annot2Color |
| Carbayo annotation data | annotCarbayo |
| Annotation of features using an annotation package | annotFeatures |
| Features annotation | annotFeaturesComp |
| Annotation of features using 'biomaRt' | annotFeaturesWithBiomaRt |
| Features annotation of an object of class IcaSet. | annotInGene |
| annotReciprocal | annotReciprocal |
| This function builds an object of class 'IcaSet'. | buildIcaSet |
| Creates an object of class MineICAParams | buildMineICAParams |
| Run of fastICA and JADE algorithms | clusterFastICARuns |
| Cluster samples from an IcaSet | clusterSamplesByComp |
| Cluster samples from an IcaSet | clusterSamplesByComp_multiple |
| Tests association between clusters of samples and variables | clusVarAnalysis |
| Comparison of IcaSet objects using correlation | compareAn |
| compareAn2graphfile | compareAn2graphfile |
| Union and intersection of contributing genes | compareGenes |
| Correlation between two matrices | cor2An |
| correl2Comp | correl2Comp |
| Retrieve and set data from IcaSet | dat dat,IcaSet-method dat<- dat<-,IcaSet,matrix-method dat<-,IcaSet-method datByGene datByGene,IcaSet-method datByGene<- datByGene<-,IcaSet,matrix-method datByGene<-,IcaSet-method geneNames geneNames,IcaSet-method |
| Carbayo expression data | dataCarbayo |
| Retrieve feature and sample values on a component stored in an 'IcaSet' object. | getComp getComp,IcaSet,character,numeric getComp,IcaSet,character,numeric-method getComp,IcaSet-method |
| Extract projection values | getProj |
| Output of 'hyperGtest' | hgOver |
| Runs an enrichment analysis per component using package 'GOstats'. | hypergeoAn |
| Class to Contain and Describe an ICA decomposition of High-Throughput Data. | Alist,IcaSet-method chipManu chipManu,IcaSet-method chipManu<- chipManu<-,IcaSet,character-method chipManu<-,IcaSet-method chipVersion chipVersion,IcaSet-method chipVersion<- chipVersion<-,IcaSet,character-method chipVersion<-,IcaSet-method class:IcaSet compNames,IcaSet-method compNames<-,IcaSet,character-method getChipManu,IcaSet-method getIndComp,IcaSet-method getLabelsComp,IcaSet-method getMart,IcaSet-method getRefSamples,IcaSet-method getTypeID,IcaSet-method IcaSet IcaSet-class indComp,IcaSet-method indComp<-,IcaSet,character-method mart mart,IcaSet-method mart<- mart<-,IcaSet,character-method mart<-,IcaSet-method organism organism,IcaSet-method organism<- organism<-,IcaSet-method refSamples refSamples,IcaSet-method refSamples<- refSamples<-,IcaSet,character-method refSamples<-,IcaSet-method setChipManu,IcaSet-method setIndComp,IcaSet-method setLabelsComp,IcaSet-method setMart,IcaSet-method setRefSamples,IcaSet-method setTypeID,IcaSet-method Slist,IcaSet-method SlistByGene,IcaSet-method typeID typeID,IcaSet-method typeID<- typeID<-,IcaSet,list-method typeID<-,IcaSet-method witGenes,IcaSet-method witGenes<-,IcaSet,character-method [ [,ANY,ANY,IcaSet-method [,IcaSet,ANY,ANY,ANY-method [,IcaSet,ANY,ANY-method [,IcaSet,ANY-method [<- [<-,IcaSet,ANY,ANY,ANY,ANY-method [<-,IcaSet,ANY,ANY,ANY-method [<-,IcaSet,ANY,ANY-method |
| IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples. | icaSetCarbayo |
| IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples. | icaSetKim |
| IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples. | icaSetRiester |
| IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples. | icaSetStransky |
| Retrieve and set component labels, indices, and witness genes from IcaSet | compNames compNames<- compNames<-,IcaSet-method getIndComp getLabelsComp getWitGenes indComp indComp<- indComp<-,IcaSet-method setIndComp setLabelsComp setWitGenes witGenes witGenes<- witGenes<-,IcaSet-method |
| Class to contain parameters for the analysis of an ICA decomposition. | Afile Afile,MineICAParams-method Afile<- Afile<-,MineICAParams,character-method Afile<-,MineICAParams-method annot2col annot2col,MineICAParams-method annot2col<- annot2col<-,MineICAParams,character-method annot2col<-,MineICAParams-method annotfile annotfile,MineICAParams-method annotfile<- annotfile<-,MineICAParams,character-method annotfile<-,MineICAParams-method class-MineICAParams class:MineICAParams datfile datfile,MineICAParams-method datfile<- datfile<-,MineICAParams,character-method datfile<-,MineICAParams-method genesPath genesPath,MineICAParams-method genesPath<- genesPath<-,ANY-method genesPath<-,MineICAParams,character-method getAfile getAnnot2col getAnnotfile getdatfile getGenesPath getPvalCutoff getResPath getSelCutoff getSfile MineICAParams pvalCutoff pvalCutoff,MineICAParams-method pvalCutoff<- pvalCutoff<-,MineICAParams,numeric-method pvalCutoff<-,MineICAParams-method resPath resPath,MineICAParams-method resPath<- resPath<-,ANY-method resPath<-,MineICAParams,character-method selCutoff selCutoff,MineICAParams-method selCutoff<- selCutoff<-,MineICAParams,numeric-method selCutoff<-,MineICAParams-method setAfile setAnnot2col setAnnotfile setdatfile setGenesPath setPvalCutoff setResPath setSelCutoff setSfile Sfile Sfile,MineICAParams-method Sfile<- Sfile<-,MineICAParams,character-method Sfile<-,MineICAParams-method [,ANY,ANY,ANY,MineICAParams-method [,ANY,ANY,MineICAParams-method [,ANY,MineICAParams-method [,MineICAParams,ANY,ANY,ANY-method [,MineICAParams,ANY,ANY-method [,MineICAParams,ANY-method [<-,MineICAParams,ANY,ANY,ANY,ANY-method [<-,MineICAParams,ANY,ANY,ANY-method [<-,MineICAParams,ANY,ANY-method |
| nbOccByGeneInComp | nbOccByGeneInComp |
| Select components the features contribute to | nbOccInComp |
| Generate node attributes | nodeAttrs |
| Plot heatmap associated with each component | plot_heatmapsOnSel |
| Plots the Gaussian fitted by 'Mclust' on several numeric vectors | plotAllMix |
| Plots graph using | plotCorGraph |
| Plots an histogram and Gaussian fitted by 'Mclust' | plotMix |
| Histograms of sample contributions for each annotation level | plotPosAnnotInComp |
| Tests association between qualitative variables and components. | qualVarAnalysis |
| Correlation between variables and components. | quantVarAnalysis |
| Relative path | relativePath |
| Run analysis of an IcaSet object | runAn |
| runCompareIcaSets | runCompareIcaSets |
| Enrichment analysis through GOstats | runEnrich |
| Run of fastICA and JADE algorithms | runICA |
| Select contributing features/genes | selectContrib selectContrib,IcaSet,numeric,character-method selectContrib,IcaSet-method selectContrib,list,numeric,ANY selectContrib,list,numeric,ANY-method |
| Selection of features based on their IQR | selectFeatures_IQR |
| selectWitnessGenes | selectWitnessGenes |
| Retrieve feature/gene projections stored in an 'IcaSet' object as a list. | Slist SlistByGene |
| Description of features using package 'biomaRt'. | writeGenes |
| writeProjByComp | writeProjByComp |
| Write rnk files containing gene projections | writeRnkFiles |
