{
  "_id": "6a1f233ab401979e73420a55",
  "Package": "RefFreeEWAS",
  "Version": "2.2",
  "Date": "2018-12-14",
  "Title": "EWAS using Reference-Free DNA Methylation Mixture Deconvolution",
  "Author": "E. Andres Houseman, Sc.D.",
  "Maintainer": "E. Andres Houseman <eahouseman@gmail.com>",
  "Description": "Reference-free method for conducting EWAS while\ndeconvoluting DNA methylation arising as mixtures of cell\ntypes.  The older method (Houseman et al.,\n2014,<doi:10.1093/bioinformatics/btu029>) is similar to\nsurrogate variable analysis (SVA and ISVA), except that it\nmakes additional use of a biological mixture assumption. The\nnewer method (Houseman et al., 2016,\n<doi:10.1186/s12859-016-1140-4>) is similar to non-negative\nmatrix factorization, with additional constraints and\nadditional utilities.",
  "License": "GPL (>= 2)",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-16 06:57:30 UTC",
    "User": "root"
  },
  "Repository": "https://jd2112.r-universe.dev",
  "Date/Publication": "2018-12-14 05:00:03 UTC",
  "RemoteUrl": "https://github.com/cran/RefFreeEWAS",
  "RemoteRef": "HEAD",
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  "MD5sum": "c23c1afc4b27d4f46f7fa597b4f0ef69",
  "_user": "jd2112",
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  "_created": "2026-05-16T06:57:30.000Z",
  "_published": "2026-06-02T18:38:50.221Z",
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    "BootRefFreeEwasModel",
    "bootstrapPairs",
    "deviance.RefFreeCellMix",
    "EstDimIC",
    "EstDimRMT",
    "ImputeByMean",
    "omnibusBoot",
    "PairsBootOneRefFreeEwasModel",
    "PairsBootRefFreeEwasModel",
    "print.BootRefFreeEwasModel",
    "print.RefFreeCellMix",
    "print.RefFreeEwasModel",
    "print.summaryBootRefFreeEwasModel",
    "projectMix",
    "RefFreeCellMix",
    "RefFreeCellMixArray",
    "RefFreeCellMixArrayDevianceBoot",
    "RefFreeCellMixArrayDevianceBoots",
    "RefFreeCellMixArrayWithCustomStart",
    "RefFreeCellMixInitialize",
    "RefFreeCellMixInitializeBySVD",
    "RefFreeEwasModel",
    "summary.BootRefFreeEwasModel",
    "summary.RefFreeCellMix",
    "svdSafe",
    "SVDwithMissing"
  ],
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      "title": "Simulated mixed-cell DNA methylation data set",
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      "file": "RefFreeEWAS.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "rfEwasExampleCovariate",
      "title": "Simulated covariate for mixed-cell DNA methylation data set",
      "object": "RefFreeEWAS",
      "file": "RefFreeEWAS.RData",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rfEwasExampleTRUEAlpha",
      "title": "True alpha intercepts used in simulation",
      "object": "RefFreeEWAS",
      "file": "RefFreeEWAS.RData",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rfEwasExampleTRUEBeta",
      "title": "True beta coefficients used in simulation (for comparison purposes)",
      "object": "RefFreeEWAS",
      "file": "RefFreeEWAS.RData",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rfEwasExampleTRUEMethDMR",
      "title": "True M matrix (cell-specific methylation values) used in simulation (for comparison purposes)",
      "object": "RefFreeEWAS",
      "file": "RefFreeEWAS.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "rfEwasExampleTRUEOmega",
      "title": "True Omega (cell mixture) coefficients used in simulation (for comparison purposes)",
      "object": "RefFreeEWAS",
      "file": "RefFreeEWAS.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 250,
      "table": true,
      "tojson": true
    },
    {
      "name": "X.HNSCC.caseStatusAge",
      "title": "HNSCC Example - Covariates",
      "object": "HNSCC",
      "file": "HNSCC.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 182,
      "table": true,
      "tojson": true
    },
    {
      "name": "Y.HNSCC.averageBetas",
      "title": "HNSCC Example - DNA Methylation Average Betas",
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      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "BootOneRefFreeEwasModel",
      "title": "One Bootstrap sample for Reference-Free EWAS Model",
      "topics": [
        "BootOneRefFreeEwasModel"
      ]
    },
    {
      "page": "BootRefFreeEwasModel",
      "title": "Bootstrap for Reference-Free EWAS Model",
      "topics": [
        "BootRefFreeEwasModel"
      ]
    },
    {
      "page": "bootstrapPairs",
      "title": "One Bootstrap Sample for Pairs",
      "topics": [
        "bootstrapPairs"
      ]
    },
    {
      "page": "deviance.RefFreeCellMix",
      "title": "deviance.RefFreeCellMix",
      "topics": [
        "deviance.RefFreeCellMix"
      ]
    },
    {
      "page": "EstDimIC",
      "title": "Dimension estimation by AIC and BIC",
      "topics": [
        "EstDimIC"
      ]
    },
    {
      "page": "EstDimRMT",
      "title": "Dimension estimation by Random Matrix Theory",
      "topics": [
        "EstDimRMT"
      ]
    },
    {
      "page": "ImputeByMean",
      "title": "Simple imputation method based on row-mean",
      "topics": [
        "ImputeByMean"
      ]
    },
    {
      "page": "omnibusBoot",
      "title": "Bootstrap-based omnibus test of significance across all features",
      "topics": [
        "omnibusBoot"
      ]
    },
    {
      "page": "PairsBootOneRefFreeEwasModel",
      "title": "One Bootstrap Sample for Reference-Free EWAS Model, Accounting for Paired Data",
      "topics": [
        "PairsBootOneRefFreeEwasModel"
      ]
    },
    {
      "page": "PairsBootRefFreeEwasModel",
      "title": "Bootstrap for Reference-Free EWAS Model, Accounting for Paired Data",
      "topics": [
        "PairsBootRefFreeEwasModel"
      ]
    },
    {
      "page": "print.BootRefFreeEwasModel",
      "title": "print.BootRefFreeEwasModel",
      "topics": [
        "print.BootRefFreeEwasModel"
      ]
    },
    {
      "page": "print.RefFreeCellMix",
      "title": "print.RefFreeCellMix",
      "topics": [
        "print.RefFreeCellMix"
      ]
    },
    {
      "page": "print.RefFreeEwasModel",
      "title": "print.RefFreeEwasModel",
      "topics": [
        "print.RefFreeEwasModel"
      ]
    },
    {
      "page": "print.summaryBootRefFreeEwasModel",
      "title": "print.summaryBootRefFreeEwasModel",
      "topics": [
        "print.summaryBootRefFreeEwasModel"
      ]
    },
    {
      "page": "projectMix",
      "title": "Cell Mixture Projection (reference-based)",
      "topics": [
        "projectMix"
      ]
    },
    {
      "page": "RefFreeCellMix",
      "title": "Reference-Free Cell Mixture Projection",
      "topics": [
        "RefFreeCellMix"
      ]
    },
    {
      "page": "RefFreeCellMixArray",
      "title": "Initialize Reference-Free Cell Mixture Projection",
      "topics": [
        "RefFreeCellMixArray"
      ]
    },
    {
      "page": "RefFreeCellMixArrayDevianceBoot",
      "title": "RefFreeCellMixArrayDevianceBoot",
      "topics": [
        "RefFreeCellMixArrayDevianceBoot"
      ]
    },
    {
      "page": "RefFreeCellMixArrayDevianceBoots",
      "title": "RefFreeCellMixArrayDevianceBoots",
      "topics": [
        "RefFreeCellMixArrayDevianceBoots"
      ]
    },
    {
      "page": "RefFreeCellMixArrayWithCustomStart",
      "title": "Reference-Free Cell Mixture Projection - Custom Initialization",
      "topics": [
        "RefFreeCellMixArrayWithCustomStart"
      ]
    },
    {
      "page": "RefFreeCellMixInitialize",
      "title": "Initialize Reference-Free Cell Mixture Projection",
      "topics": [
        "RefFreeCellMixInitialize"
      ]
    },
    {
      "page": "RefFreeCellMixInitializeBySVD",
      "title": "Initialize Reference-Free Cell Mixture Projection by SVD",
      "topics": [
        "RefFreeCellMixInitializeBySVD"
      ]
    },
    {
      "page": "RefFreeEwasModel",
      "title": "Reference-Free EWAS Model",
      "topics": [
        "RefFreeEwasModel"
      ]
    },
    {
      "page": "rfEwasExampleBetaValues",
      "title": "Simulated mixed-cell DNA methylation data set",
      "topics": [
        "rfEwasExampleBetaValues"
      ]
    },
    {
      "page": "rfEwasExampleCovariate",
      "title": "Simulated covariate for mixed-cell DNA methylation data set",
      "topics": [
        "rfEwasExampleCovariate"
      ]
    },
    {
      "page": "rfEwasExampleTRUEAlpha",
      "title": "True alpha intercepts used in simulation",
      "topics": [
        "rfEwasExampleTRUEAlpha"
      ]
    },
    {
      "page": "rfEwasExampleTRUEBeta",
      "title": "True beta coefficients used in simulation (for comparison purposes)",
      "topics": [
        "rfEwasExampleTRUEBeta"
      ]
    },
    {
      "page": "rfEwasExampleTRUEMethDMR",
      "title": "True M matrix (cell-specific methylation values) used in simulation (for comparison purposes)",
      "topics": [
        "rfEwasExampleTRUEMethDMR"
      ]
    },
    {
      "page": "rfEwasExampleTRUEOmega",
      "title": "True Omega (cell mixture) coefficients used in simulation (for comparison purposes)",
      "topics": [
        "rfEwasExampleTRUEOmega"
      ]
    },
    {
      "page": "summary.BootRefFreeEwasModel",
      "title": "summary.BootRefFreeEwasModel",
      "topics": [
        "summary.BootRefFreeEwasModel"
      ]
    },
    {
      "page": "summary.RefFreeCellMix",
      "title": "summary.RefFreeCellMix",
      "topics": [
        "summary.RefFreeCellMix"
      ]
    },
    {
      "page": "svdSafe",
      "title": "Safe SVD-like matrix decomposition",
      "topics": [
        "svdSafe"
      ]
    },
    {
      "page": "SVDwithMissing",
      "title": "SVD with missing values",
      "topics": [
        "SVDwithMissing"
      ]
    },
    {
      "page": "X.HNSCC.caseStatusAge",
      "title": "HNSCC Example - Covariates",
      "topics": [
        "X.HNSCC.caseStatusAge"
      ]
    },
    {
      "page": "Y.HNSCC.averageBetas",
      "title": "HNSCC Example - DNA Methylation Average Betas",
      "topics": [
        "Y.HNSCC.averageBetas"
      ]
    }
  ],
  "_rundeps": [
    "quadprog"
  ],
  "_score": 2.1205739312058496,
  "_indexed": false,
  "_nocasepkg": "reffreeewas",
  "_universes": [
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      "fileid": "4b8bd65572fe2154baeed036481d264bad76c2fc54637fb9248ebc981a6ecc23",
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