{
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  "Type": "Package",
  "Title": "Analysis of an ICA decomposition obtained on genomics data",
  "Version": "1.50.0",
  "Date": "2012-03-16",
  "Author": "Anne Biton",
  "Maintainer": "Anne Biton <anne.biton@gmail.com>",
  "Description": "The goal of MineICA is to perform Independent Component\nAnalysis (ICA) on multiple transcriptome datasets, integrating\nadditional data (e.g molecular, clinical and pathological).\nThis Integrative ICA helps the biological interpretation of the\ncomponents by studying their association with variables (e.g\nsample annotations) and gene sets, and enables the comparison\nof components from different datasets using correlation-based\ngraph.",
  "License": "GPL-2",
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  "Date/Publication": "2025-10-29 14:13:40 UTC",
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      "title": "IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.",
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      "file": "icaSetCarbayo.rda",
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      "table": false,
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      "title": "Retrieve and set Source S and Mixing matrix A from IcaSet",
      "topics": [
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        "A,IcaSet-method",
        "A<-",
        "A<-,IcaSet,data.frame-method",
        "A<-,IcaSet-method",
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        "S<-,IcaSet-method",
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        "setS<-",
        "setSByGene,IcaSet-method",
        "setSByGene<-"
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    },
    {
      "page": "Alist",
      "title": "Retrieve sample contributions stored in an 'IcaSet' object as a list.",
      "topics": [
        "Alist"
      ]
    },
    {
      "page": "annot2Color",
      "title": "Association of a colour with each annotation level",
      "topics": [
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    },
    {
      "page": "annotCarbayo",
      "title": "Carbayo annotation data",
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      "topics": [
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      "topics": [
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      "title": "annotReciprocal",
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    {
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      "title": "Cluster samples from an IcaSet",
      "topics": [
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    },
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      "title": "Tests association between clusters of samples and variables",
      "topics": [
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    },
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      "title": "Comparison of IcaSet objects using correlation",
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      "title": "compareAn2graphfile",
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      "topics": [
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    {
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      "topics": [
        "correl2Comp"
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      "page": "dat",
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        "dat,IcaSet-method",
        "dat<-",
        "dat<-,IcaSet,matrix-method",
        "dat<-,IcaSet-method",
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        "datByGene<-",
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        "datByGene<-,IcaSet-method",
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      "topics": [
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    },
    {
      "page": "getComp",
      "title": "Retrieve feature and sample values on a component stored in an 'IcaSet' object.",
      "topics": [
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        "getComp,IcaSet,character,numeric",
        "getComp,IcaSet,character,numeric-method",
        "getComp,IcaSet-method"
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      "page": "getProj",
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      "topics": [
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      ]
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      "page": "hgOver",
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      "topics": [
        "hgOver"
      ]
    },
    {
      "page": "hypergeoAn",
      "title": "Runs an enrichment analysis per component using package 'GOstats'.",
      "topics": [
        "hypergeoAn"
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    {
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      "title": "Class to Contain and Describe an ICA decomposition of High-Throughput Data.",
      "topics": [
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        "chipManu",
        "chipManu,IcaSet-method",
        "chipManu<-",
        "chipManu<-,IcaSet,character-method",
        "chipManu<-,IcaSet-method",
        "chipVersion",
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        "chipVersion<-,IcaSet-method",
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        "compNames<-,IcaSet,character-method",
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        "getLabelsComp,IcaSet-method",
        "getMart,IcaSet-method",
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        "getTypeID,IcaSet-method",
        "IcaSet",
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        "indComp,IcaSet-method",
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        "mart",
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        "mart<-",
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        "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",
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        "typeID,IcaSet-method",
        "typeID<-",
        "typeID<-,IcaSet,list-method",
        "typeID<-,IcaSet-method",
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        "witGenes<-,IcaSet,character-method",
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        "[<-,IcaSet,ANY,ANY,ANY-method",
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    {
      "page": "icaSetCarbayo",
      "title": "IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.",
      "topics": [
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    },
    {
      "page": "icaSetKim",
      "title": "IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.",
      "topics": [
        "icaSetKim"
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    },
    {
      "page": "icaSetRiester",
      "title": "IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.",
      "topics": [
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    },
    {
      "page": "icaSetStransky",
      "title": "IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.",
      "topics": [
        "icaSetStransky"
      ]
    },
    {
      "page": "indComp",
      "title": "Retrieve and set component labels, indices, and witness genes from IcaSet",
      "topics": [
        "compNames",
        "compNames<-",
        "compNames<-,IcaSet-method",
        "getIndComp",
        "getLabelsComp",
        "getWitGenes",
        "indComp",
        "indComp<-",
        "indComp<-,IcaSet-method",
        "setIndComp",
        "setLabelsComp",
        "setWitGenes",
        "witGenes",
        "witGenes<-",
        "witGenes<-,IcaSet-method"
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    },
    {
      "page": "class-MineICAParams",
      "title": "Class to contain parameters for the analysis of an ICA decomposition.",
      "topics": [
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        "Afile,MineICAParams-method",
        "Afile<-",
        "Afile<-,MineICAParams,character-method",
        "Afile<-,MineICAParams-method",
        "annot2col",
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        "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",
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      "page": "nbOccInComp",
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      "page": "nodeAttrs",
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      "page": "plot_heatmapsOnSel",
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      "page": "plotAllMix",
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      "page": "plotCorGraph",
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      "page": "qualVarAnalysis",
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      "page": "runAn",
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      "page": "runCompareIcaSets",
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      "page": "runEnrich",
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      "page": "runICA",
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      "page": "selectContrib",
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