{
  "_id": "6a1fde3fb401979e73438a6e",
  "Package": "limpca",
  "Type": "Package",
  "Title": "An R package for the linear modeling of high-dimensional\ndesigned data based on ASCA/APCA family of methods",
  "Version": "1.9.0",
  "Authors@R": "c(person(\"Bernadette\", \"Govaerts\", role = c(\"aut\", \"ths\"),\nemail = \"bernadette.govaerts@uclouvain.be\"),\nperson(\"Sebastien\",\"Franceschini\", role = \"ctb\",\nemail=\"sfranceschini@uliege.be\"),\nperson(\"Robin\",\"van Oirbeek\", role = \"ctb\",\nemail=\"robin.vanoirbeek@gmail.com\"),\nperson(\"Michel\",\"Thiel\", role = \"aut\",\nemail=\"michel.thiel@uclouvain.be\"),\nperson(\"Pascal\",\"de Tullio\", role = \"dtc\",\nemail=\"pdetullio@uliege.be\"),\nperson(\"Manon\",\"Martin\", role = c(\"aut\", \"cre\"),\nemail=\"manon.martin@uclouvain.be\",\ncomment = c(ORCID = \"0000-0003-4800-0942\")),\nperson(\"Nadia\", \"Benaiche\", role = \"ctb\",\nemail = \"nadia.benaiche@student.uclouvain.be\"))",
  "Description": "This package has for objectives to provide a method to\nmake Linear Models for high-dimensional designed data. limpca\napplies a GLM (General Linear Model) version of ASCA and APCA\nto analyse multivariate sample profiles generated by an\nexperimental design. ASCA/APCA provide powerful visualization\ntools for multivariate structures in the space of each effect\nof the statistical model linked to the experimental design and\ncontrarily to MANOVA, it can deal with mutlivariate datasets\nhaving more variables than observations. This method can handle\nunbalanced design.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
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  "VignetteBuilder": "knitr",
  "biocViews": "StatisticalMethod, PrincipalComponent, Regression,\nVisualization, ExperimentalDesign, MultipleComparison,\nGeneExpression, Metabolomics",
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  "Roxygen": "list(markdown=TRUE)",
  "BugReports": "https://github.com/ManonMartin/limpca/issues",
  "URL": "https://github.com/ManonMartin/limpca,\nhttps://manonmartin.github.io/limpca/",
  "Config/testthat/edition": "3",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:03:08 UTC",
  "RemoteUrl": "https://github.com/bioc/limpca",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 07:49:24 UTC",
    "User": "root"
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  "Author": "Bernadette Govaerts [aut, ths],\nSebastien Franceschini [ctb],\nRobin van Oirbeek [ctb],\nMichel Thiel [aut],\nPascal de Tullio [dtc],\nManon Martin [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4800-0942>),\nNadia Benaiche [ctb]",
  "Maintainer": "Manon Martin <manon.martin@uclouvain.be>",
  "MD5sum": "e4813cee33b81ebe51c0e5d0f238dbdc",
  "_user": "bioc",
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  "_created": "2026-06-03T07:49:24.000Z",
  "_published": "2026-06-03T07:56:47.479Z",
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  "_updates": [
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  "_devurl": "https://github.com/manonmartin/limpca",
  "_pkgdown": "https://manonmartin.github.io/limpca/",
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  "_assets": [
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    "extra/citation.json",
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  "_homeurl": "https://github.com/manonmartin/limpca",
  "_realowner": "bioc",
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  "_exports": [
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    "lmpBootstrapTests",
    "lmpContributions",
    "lmpEffectMatrices",
    "lmpEffectPlot",
    "lmpLoading1dPlot",
    "lmpLoading2dPlot",
    "lmpModelMatrix",
    "lmpPcaEffects",
    "lmpScorePlot",
    "lmpScoreScatterPlotM",
    "lmpScreePlot",
    "pcaBySvd",
    "pcaLoading1dPlot",
    "pcaLoading2dPlot",
    "pcaScorePlot",
    "pcaScreePlot",
    "plotDesign",
    "plotLine",
    "plotMeans",
    "plotScatter",
    "plotScatterM"
  ],
  "_datasets": [
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      "title": "trout: the Rainbow trouts transcriptomic dataset",
      "object": "trout",
      "file": "trout.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "UCH",
      "title": "UCH: the Urine Citrate-Hippurate metabolomic dataset",
      "object": "UCH",
      "file": "UCH.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "data2lmpDataList",
      "title": "Converts data to a lmpDataList.",
      "topics": [
        "data2LmpDataList"
      ]
    },
    {
      "page": "limpca",
      "title": "Linear modeling of high-dimensional designed data based on ASCA/APCA family of methods",
      "topics": [
        "limpca"
      ]
    },
    {
      "page": "lmpBootstrapTests",
      "title": "Tests the significance of model effects by bootstrap.",
      "topics": [
        "lmpBootstrapTests"
      ]
    },
    {
      "page": "lmpContributions",
      "title": "Summary of the contributions of each effect",
      "topics": [
        "lmpContributions"
      ]
    },
    {
      "page": "lmpEffectMatrices",
      "title": "Computes the effect matrices",
      "topics": [
        "lmpEffectMatrices"
      ]
    },
    {
      "page": "lmpEffectPlot",
      "title": "Effect plot",
      "topics": [
        "lmpEffectPlot"
      ]
    },
    {
      "page": "lmpLoading1dPlot",
      "title": "Loadings represented on a line plot.",
      "topics": [
        "lmpLoading1dPlot"
      ]
    },
    {
      "page": "lmpLoading2dPlot",
      "title": "Loading plots on a 2D scatter plot",
      "topics": [
        "lmpLoading2dPlot"
      ]
    },
    {
      "page": "lmpModelMatrix",
      "title": "Creates the model matrix 'X'",
      "topics": [
        "lmpModelMatrix"
      ]
    },
    {
      "page": "lmpPcaEffects",
      "title": "PCA on the effect matrices",
      "topics": [
        "lmpPcaEffects"
      ]
    },
    {
      "page": "lmpScorePlot",
      "title": "Score plots of effect matrices",
      "topics": [
        "lmpScorePlot"
      ]
    },
    {
      "page": "lmpScoreScatterPlotM",
      "title": "Scatterplot matrix of effect matrices scores",
      "topics": [
        "lmpScoreScatterPlotM"
      ]
    },
    {
      "page": "lmpScreePlot",
      "title": "Scree Plot",
      "topics": [
        "lmpScreePlot"
      ]
    },
    {
      "page": "pcaBySvd",
      "title": "Singular Value Decomposition for PCA analysis",
      "topics": [
        "pcaBySvd"
      ]
    },
    {
      "page": "pcaLoading1dPlot",
      "title": "Loadings represented on a line plot.",
      "topics": [
        "pcaLoading1dPlot"
      ]
    },
    {
      "page": "pcaLoading2dPlot",
      "title": "Loading plots on a 2D scatter plot",
      "topics": [
        "pcaLoading2dPlot"
      ]
    },
    {
      "page": "pcaScorePlot",
      "title": "Score plots",
      "topics": [
        "pcaScorePlot"
      ]
    },
    {
      "page": "pcaScreePlot",
      "title": "Scree Plot",
      "topics": [
        "pcaScreePlot"
      ]
    },
    {
      "page": "plotDesign",
      "title": "Plot of the design matrix",
      "topics": [
        "plotDesign"
      ]
    },
    {
      "page": "plotLine",
      "title": "Line plot",
      "topics": [
        "plotLine"
      ]
    },
    {
      "page": "plotMeans",
      "title": "Means plot",
      "topics": [
        "plotMeans"
      ]
    },
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      "page": "plotScatter",
      "title": "Scatter plot",
      "topics": [
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      ]
    },
    {
      "page": "plotScatterM",
      "title": "Scatter plot matrix",
      "topics": [
        "plotScatterM"
      ]
    },
    {
      "page": "trout",
      "title": "trout: the Rainbow trouts transcriptomic dataset",
      "topics": [
        "trout"
      ]
    },
    {
      "page": "UCH",
      "title": "UCH: the Urine Citrate-Hippurate metabolomic dataset",
      "topics": [
        "UCH"
      ]
    }
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      "source": "Trout.Rmd",
      "filename": "Trout.html",
      "title": "Application of limpca on the Trout transcriptomic dataset.",
      "author": "Benaiche Nadia, Bernadette Govaerts",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation and loading of the limpca package",
        "Data and model presentation",
        "Data import and exploration",
        "Data import and design visualization",
        "Principal Component Analysis of row data",
        "Log10 transformation of the data and new PCA",
        "New PCA without the outliers",
        "Mean agregation by aquarium and scaling",
        "Exploration of aggregated data",
        "Design",
        "Example of lineplot of the responses for two observations",
        "PCA aggregated data",
        "Score plots",
        "1D Loading plots",
        "2D Loading plots",
        "Scatterplot matrix of all 15 responses",
        "GLM decomposition",
        "Model matrix X generation",
        "Computation of effect matrices and importances",
        "Bootstrap test of effect significance",
        "ASCA and APCA",
        "ASCA",
        "PCA decomposition of effect matrices",
        "Contributions",
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        "Day effect",
        "Treatment effect",
        "Day:Treatment effect",
        "Combined Day+Treatment+Day:Treatment effect",
        "Residual matrix decomposition",
        "Effect plots on scores",
        "APCA",
        "Univariate ANOVA",
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        "FDR corrected p_values (q-values)",
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      "created": "2022-12-07 14:43:54",
      "modified": "2024-04-26 11:03:52",
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      "filename": "UCH.html",
      "title": "Application of limpca on the UCH metabolomics dataset.",
      "author": "Benaiche Nadia, Sébastien Franceschini, Martin Manon, Thiel Michel, Govaerts Bernadette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation and loading of the limpca package",
        "Data import",
        "Data exploration",
        "Design",
        "Outcomes visualization",
        "plotLine function",
        "plotScatter function",
        "plotScatterM function",
        "plotMeans function",
        "PCA",
        "Application of ASCA+ and APCA+",
        "Model estimation and effect matrix decomposition",
        "Model formula",
        "Model matrix generation",
        "Model estimation and effect matrices decomposition",
        "Effects importance",
        "Bootstrap tests and quantification of effects importance",
        "ASCA/APCA/ASCA-E decomposition",
        "ASCA",
        "Contributions",
        "Scores and loadings Plots",
        "Main effects",
        "Interaction Hippurate:Time",
        "Combination of effects Hippurate+Time+Hippurate:Time",
        "Model residuals",
        "Other graphs",
        "Scores scatter plot",
        "2D Loadings",
        "Effects plot",
        "Main effects for Hippurate",
        "APCA",
        "Scores Plot",
        "Loadings plot",
        "ASCA-E",
        "sessionInfo",
        "References"
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      "created": "2022-09-20 14:46:27",
      "modified": "2024-04-26 11:03:52",
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    {
      "source": "limpca.Rmd",
      "filename": "limpca.html",
      "title": "Get started with limpca.",
      "author": "Benaiche Nadia, Sébastien Franceschini, Martin Manon, Thiel Michel, Govaerts Bernadette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "About the package",
        "Vignettes description",
        "Installation and loading of the limpca package",
        "Short application on the UCH dataset",
        "Data object",
        "Data visualisation",
        "PCA",
        "Model estimation and effect matrix decomposition",
        "Effect matrix test of significance and importance measure",
        "ASCA decomposition",
        "sessionInfo"
      ],
      "created": "2022-12-06 14:04:20",
      "modified": "2024-04-26 12:09:57",
      "commits": 10
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