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    {
      "page": "MetNet-package",
      "title": "Inferring metabolic networks from untargeted high-resolution mass spectrometry data",
      "topics": [
        "MetNet-package",
        "MetNet"
      ]
    },
    {
      "page": "dot-AdjacencyMatrix",
      "title": "Create S4 class AdjacencyMatrix",
      "topics": [
        ".AdjacencyMatrix"
      ]
    },
    {
      "page": "dot-assays_have_identical_colnames_rownames",
      "title": "Check if all the assays in the `AdjacencyMatrix` object have identical colnames and rownames",
      "topics": [
        ".assays_have_identical_colnames_rownames"
      ]
    },
    {
      "page": "dot-assays_have_identical_dimnames",
      "title": "Check if the assays in the `AdjacencyMatrix` object have identical dimnames",
      "topics": [
        ".assays_have_identical_dimnames"
      ]
    },
    {
      "page": "addSpectralSimilarity",
      "title": "Adding a spectral similarity matrix to the \"structural\" `AdjacencyMatrix`",
      "topics": [
        "addSpectralSimilarity"
      ]
    },
    {
      "page": "addToList",
      "title": "Add adjacency matrix to list",
      "topics": [
        "addToList"
      ]
    },
    {
      "page": "AdjacencyMatrix",
      "title": "Wrapper to create an instance of S4 class AdjacencyMatrix",
      "topics": [
        "AdjacencyMatrix"
      ]
    },
    {
      "page": "AdjacencyMatrix-class",
      "title": "Methods for `AdjacencyMatrix` objects",
      "topics": [
        "AdjacencyMatrix-class",
        "as.data.frame",
        "as.data.frame,AdjacencyMatrix-method",
        "dim",
        "dim,AdjacencyMatrix-method",
        "directed",
        "directed,AdjacencyMatrix-method",
        "length,AdjacencyMatrix-method",
        "show",
        "show,AdjacencyMatrix-method",
        "thresholded",
        "thresholded,AdjacencyMatrix-method",
        "type",
        "type,AdjacencyMatrix-method"
      ]
    },
    {
      "page": "AllGenerics",
      "title": "Placeholder for generics functions documentation",
      "topics": [
        "AllGenerics"
      ]
    },
    {
      "page": "aracne",
      "title": "Create an adjacency matrix based on algorithm for the reconstruction of accurate cellular networks",
      "topics": [
        "aracne"
      ]
    },
    {
      "page": "bayes",
      "title": "Create an adjacency matrix based on score-based structure learning algorithm",
      "topics": [
        "bayes"
      ]
    },
    {
      "page": "clr",
      "title": "Create an adjacency matrix based on context likelihood or relatedness network",
      "topics": [
        "clr"
      ]
    },
    {
      "page": "combine",
      "title": "Combine structural and statistical `AdjacencyMatrix` objects",
      "topics": [
        "combine"
      ]
    },
    {
      "page": "correlation",
      "title": "Create an adjacency matrix based on correlation",
      "topics": [
        "correlation"
      ]
    },
    {
      "page": "getLinks",
      "title": "Write an adjacency matrix to a `data.frame`",
      "topics": [
        "getLinks"
      ]
    },
    {
      "page": "lasso",
      "title": "Create an adjacency matrix based on LASSO",
      "topics": [
        "lasso"
      ]
    },
    {
      "page": "mat_test",
      "title": "Example data for 'MetNet': unit tests",
      "topics": [
        "mat_test"
      ]
    },
    {
      "page": "mat_test_z",
      "title": "Example data for 'MetNet': unit tests",
      "topics": [
        "mat_test_z"
      ]
    },
    {
      "page": "ms2_test",
      "title": "Spectra data to test addSpectralSimilarity",
      "topics": [
        "ms2_test",
        "sps_sub"
      ]
    },
    {
      "page": "mz_summary",
      "title": "Create a summary from adjacency list containing mass differences",
      "topics": [
        "mz_summary"
      ]
    },
    {
      "page": "mz_vis",
      "title": "Visualize mass difference distribution",
      "topics": [
        "mz_vis"
      ]
    },
    {
      "page": "partialCorrelation",
      "title": "Calculate the partial correlation and p-values",
      "topics": [
        "partialCorrelation"
      ]
    },
    {
      "page": "peaklist",
      "title": "Example data for 'MetNet': data input",
      "topics": [
        "peaklist"
      ]
    },
    {
      "page": "randomForest",
      "title": "Create an adjacency matrix based on random forest",
      "topics": [
        "randomForest"
      ]
    },
    {
      "page": "rtCorrection",
      "title": "Correct connections in the structural adjacency matrices by retention time",
      "topics": [
        "rtCorrection"
      ]
    },
    {
      "page": "spectra_matrix",
      "title": "Spectra data to test addSpectralSimilarity",
      "topics": [
        "spectra_matrix"
      ]
    },
    {
      "page": "statistical",
      "title": "Create an `AdjacencyMatrix` object containing assays of adjacency matrices from statistical methods",
      "topics": [
        "statistical"
      ]
    },
    {
      "page": "structural",
      "title": "Create adjacency matrix based on m/z (molecular weight) difference",
      "topics": [
        "structural"
      ]
    },
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      "page": "threshold",
      "title": "Threshold the statistical adjacency or spectral similarity matrices",
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      "page": "topKnet",
      "title": "Return consensus ranks from a matrix containing ranks",
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      "page": "x_annotation",
      "title": "Example annotation for 'MetNet': data input",
      "topics": [
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      "page": "x_test",
      "title": "Example data for 'MetNet': data input",
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