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      "fields": [],
      "rows": 300,
      "table": true,
      "tojson": true
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    {
      "name": "ed",
      "title": "STATegRa data",
      "object": "STATegRa_S1",
      "file": "STATegRa_S1.rda",
      "class": [
        "data.frame"
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      "fields": [
        "classname"
      ],
      "rows": 169,
      "table": true,
      "tojson": true
    },
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      "name": "ed.PCA",
      "title": "STATegRa data",
      "object": "STATegRa_S3",
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        "classname"
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      "table": true,
      "tojson": true
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      "object": "STATegRa_S2",
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        "Var1",
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      "name": "TCGA_BRCA_Data",
      "title": "STATegRa data",
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        "list"
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      "tojson": false
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    {
      "page": "bioDist",
      "title": "bioDist",
      "topics": [
        "bioDist",
        "bioDist,character,character,bioMap,ExpressionSet,ExpressionSet-method"
      ]
    },
    {
      "page": "bioDistclass",
      "title": "bioDistclass",
      "topics": [
        "bioDistclass"
      ]
    },
    {
      "page": "bioDistFeature",
      "title": "bioDistFeature",
      "topics": [
        "bioDistFeature",
        "bioDistFeature,character,list,numeric-method"
      ]
    },
    {
      "page": "bioDistFeaturePlot",
      "title": "bioDistFeaturePlot",
      "topics": [
        "bioDistFeaturePlot"
      ]
    },
    {
      "page": "bioDistW",
      "title": "bioDistW",
      "topics": [
        "bioDistW",
        "bioDistW,character,list,matrix-method"
      ]
    },
    {
      "page": "bioDistWPlot",
      "title": "bioDistWPlot",
      "topics": [
        "bioDistWPlot",
        "bioDistWPlot,character,list,character-method"
      ]
    },
    {
      "page": "bioMap",
      "title": "bioMap",
      "topics": [
        "bioMap"
      ]
    },
    {
      "page": "caClass-class",
      "title": "caClass",
      "topics": [
        "caClass-class"
      ]
    },
    {
      "page": "combiningMappings",
      "title": "combiningMappings, combining several mappings for use in the omicsNPC function",
      "topics": [
        "combiningMappings"
      ]
    },
    {
      "page": "createOmicsExpressionSet",
      "title": "createOmicsExpressionSet",
      "topics": [
        "createOmicsExpressionSet",
        "createOmicsExpressionSet,matrix-method"
      ]
    },
    {
      "page": "getInitialData",
      "title": "Retrieve initial data from caClass objects",
      "topics": [
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        "getInitialData,caClass-method"
      ]
    },
    {
      "page": "getLoadings",
      "title": "Retrieve component analysis loadings",
      "topics": [
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        "getLoadings,caClass-method"
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    },
    {
      "page": "getMethodInfo",
      "title": "Retrieve information about component analysis method",
      "topics": [
        "getMethodInfo",
        "getMethodInfo,caClass-method"
      ]
    },
    {
      "page": "getPreprocessing",
      "title": "Retrieve information about preprocessing",
      "topics": [
        "getPreprocessing",
        "getPreprocessing,caClass-method"
      ]
    },
    {
      "page": "getScores",
      "title": "Retrieve component analysis scores",
      "topics": [
        "getScores",
        "getScores,caClass-method"
      ]
    },
    {
      "page": "getVAF",
      "title": "Retrieve information abotut VAF",
      "topics": [
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        "getVAF,caClass-method"
      ]
    },
    {
      "page": "holistOmics",
      "title": "HolistOmics an application of NPC on omics datasets",
      "topics": [
        "holistOmics",
        "holistOmics,list,character-method"
      ]
    },
    {
      "page": "modelSelection",
      "title": "Find optimal common and distinctive components",
      "topics": [
        "modelSelection",
        "modelSelection,list,numeric,character-method"
      ]
    },
    {
      "page": "omicsCompAnalysis",
      "title": "Components analysis for multiple objects",
      "topics": [
        "omicsCompAnalysis",
        "omicsCompAnalysis,list,character,character,numeric,numeric-method"
      ]
    },
    {
      "page": "omicsNPC",
      "title": "omicsNPC, applying the Non-Parametric Combination (NPC) on omics datasets",
      "topics": [
        "omicsNPC",
        "omicsNPC,list,data.frame-method",
        "omicsNPC,list,missing-method"
      ]
    },
    {
      "page": "plotRes",
      "title": "Plot component analysis results",
      "topics": [
        "plotRes",
        "plotRes,caClass,numeric,character,character,logical-method"
      ]
    },
    {
      "page": "plotVAF",
      "title": "Plot VAF (Variance Explained For) from Component Analysis",
      "topics": [
        "plotVAF",
        "plotVAF,caClass-method"
      ]
    },
    {
      "page": "STATegRa",
      "title": "STATegRa",
      "topics": [
        "STATegRa-package",
        "STATegRa"
      ]
    },
    {
      "page": "STATegRa_data",
      "title": "STATegRa data",
      "topics": [
        "Block1",
        "Block1.PCA",
        "Block2",
        "Block2.PCA",
        "ed",
        "ed.PCA",
        "mapdata",
        "STATegRa_data"
      ]
    },
    {
      "page": "STATegRa_data_TCGA_BRCA",
      "title": "STATegRa data",
      "topics": [
        "STATegRa_data_TCGA_BRCA",
        "TCGA_BRCA_Data"
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    },
    {
      "page": "STATegRa-defunct",
      "title": "Defunct functions in STATegRa",
      "topics": [
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    },
    {
      "page": "STATegRaUsersGuide",
      "title": "STATegRaUsersGuide",
      "topics": [
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      ]
    }
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    "affyio",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "bitops",
    "calibrate",
    "caTools",
    "cli",
    "codetools",
    "cpp11",
    "edgeR",
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    "generics",
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    "gplots",
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    "gtable",
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    "KernSmooth",
    "labeling",
    "lifecycle",
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    "preprocessCore",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "statmod",
    "vctrs",
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    "withr"
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  "_vignettes": [
    {
      "source": "STATegRa.Rmd",
      "filename": "STATegRa.html",
      "title": "STATegRa User's Guide",
      "author": "The STATegra Consortium",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting Started",
        "Omics Component Analysis",
        "Overview",
        "Usage",
        "Worked example",
        "Load data",
        "Model Selection",
        "Component Analysis",
        "Plot results",
        "Omics Clustering",
        "The Problem",
        "The OmicsClustering Approach",
        "Loading the data",
        "Computing the distance between genes by using mRNA data: the bioDistclass class",
        "Loading the map between miRNA and genes: the bioMap class",
        "miRNA-Surrogate gene Distances: the bioDist function",
        "Computing weighted distances: the bioDistW function",
        "Plots",
        "Plotting the feature distance of each weighted combination",
        "Plotting associated features",
        "OmicsClustering Requirements",
        "omicsNPC",
        "The NPC Approach",
        "Setting the dataTypes variable",
        "Setting the combMethods variable",
        "Setting the numPerms, numCores and verbose variables",
        "Run omicsNPC analysis.",
        "References"
      ],
      "created": "2014-10-08 00:21:41",
      "modified": "2018-04-24 09:26:26",
      "commits": 4
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