{
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  "Package": "CoGAPS",
  "Version": "3.33.0",
  "Date": "2025-03-11",
  "Title": "Coordinated Gene Activity in Pattern Sets",
  "Author": "Jeanette Johnson, Ashley Tsang, Jacob Mitchell, Thomas Sherman,\nWai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey,\nGenevieve Stein-O'Brien, Michael Considine, Maggie Wodicka,\nJohn Stansfield, Shawn Sivy, Carlo Colantuoni, Alexander\nFavorov, Mike Ochs, Elana Fertig",
  "Description": "Coordinated Gene Activity in Pattern Sets (CoGAPS)\nimplements a Bayesian MCMC matrix factorization algorithm,\nGAPS, and links it to gene set statistic methods to infer\nbiological process activity.  It can be used to perform sparse\nmatrix factorization on any data, and when this data represents\nbiomolecules, to do gene set analysis.",
  "Maintainer": "Elana J. Fertig <ejfertig@jhmi.edu>, Thomas D. Sherman\n<tomsherman159@gmail.com>, Jeanette Johnson\n<jjohn450@jhmi.edu>, Dmitrijs Lvovs <dlvovs1@jh.edu>",
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  "License": "BSD_3_clause + file LICENSE",
  "biocViews": "GeneExpression, Transcription, GeneSetEnrichment,\nDifferentialExpression, Bayesian, Clustering, TimeCourse,\nRNASeq, Microarray, MultipleComparison, DimensionReduction,\nImmunoOncology",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:45 UTC",
  "RemoteUrl": "https://github.com/bioc/CoGAPS",
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  "_published": "2026-05-30T12:46:27.968Z",
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    "getParam",
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    "getPatternMatrix",
    "getRetinaSubset",
    "getSampleFactors",
    "getSubsets",
    "getUnmatchedPatterns",
    "getVersion",
    "GWCoGAPS",
    "MANOVA",
    "patternMarkers",
    "plotPatternGeneSet",
    "plotPatternMarkers",
    "plotResiduals",
    "reconstructGene",
    "scCoGAPS",
    "setAnnotationWeights",
    "setDistributedParams",
    "setFixedPatterns",
    "setParam",
    "toCSV"
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      "title": "GIST gene expression data from Ochs et al. (2009)",
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      "class": [
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        "IM04",
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      "table": true,
      "tojson": true
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        "IM48"
      ],
      "rows": 1363,
      "table": true,
      "tojson": true
    },
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      "title": "CoGAPS result from running on GIST dataset",
      "object": "GIST",
      "file": "GIST.RData",
      "class": [
        "CogapsResult"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "title": "GIST gene expression uncertainty matrix from Ochs et al. (2009)",
      "object": "GIST",
      "file": "GIST.RData",
      "class": [
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        "array"
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        "IM02",
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        "IM48"
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      "rows": 1363,
      "table": true,
      "tojson": true
    },
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      "title": "Toy example to run CoGAPS on.",
      "object": "modsimdata",
      "file": "modsimdata.rda",
      "class": [
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        "V2",
        "V3",
        "V4",
        "V5",
        "V6",
        "V7",
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        "V9",
        "V10",
        "V11",
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        "V15",
        "V16",
        "V17",
        "V18",
        "V19",
        "V20"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "modsimresult",
      "title": "Result of applying CoGAPS on the Toy example.",
      "object": "modsimresult",
      "file": "modsimresult.rda",
      "class": [
        "CogapsResult"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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  "_help": [
    {
      "page": "CoGAPS-package",
      "title": "CoGAPS: Coordinated Gene Activity in Pattern Sets",
      "topics": [
        "CoGAPS-package"
      ]
    },
    {
      "page": "binaryA-methods",
      "title": "binary heatmap for standardized feature matrix",
      "topics": [
        "binaryA",
        "binaryA,CogapsResult-method"
      ]
    },
    {
      "page": "buildReport",
      "title": "Information About Package Compilation",
      "topics": [
        "buildReport"
      ]
    },
    {
      "page": "calcCoGAPSStat-methods",
      "title": "calculate statistic on sets of measurements (genes) or samples",
      "topics": [
        "calcCoGAPSStat",
        "calcCoGAPSStat,CogapsResult-method"
      ]
    },
    {
      "page": "calcGeneGSStat-methods",
      "title": "probability gene belongs in gene set",
      "topics": [
        "calcGeneGSStat",
        "calcGeneGSStat,CogapsResult-method"
      ]
    },
    {
      "page": "calcZ-methods",
      "title": "compute z-score matrix",
      "topics": [
        "calcZ",
        "calcZ,CogapsResult-method"
      ]
    },
    {
      "page": "checkpointsEnabled",
      "title": "Check if package was built with checkpoints enabled",
      "topics": [
        "checkpointsEnabled"
      ]
    },
    {
      "page": "CoGAPS",
      "title": "CoGAPS Matrix Factorization Algorithm",
      "topics": [
        "CoGAPS"
      ]
    },
    {
      "page": "CogapsParams",
      "title": "CogapsParams constructor",
      "topics": [
        "CogapsParams"
      ]
    },
    {
      "page": "CogapsParams-class",
      "title": "CogapsParams",
      "topics": [
        "CogapsParams-class"
      ]
    },
    {
      "page": "CogapsResult-class",
      "title": "CogapsResult",
      "topics": [
        "CogapsResult-class"
      ]
    },
    {
      "page": "compiledWithOpenMPSupport",
      "title": "Check if compiler supported OpenMP",
      "topics": [
        "compiledWithOpenMPSupport"
      ]
    },
    {
      "page": "computeGeneGSProb-methods",
      "title": "compute gene probability",
      "topics": [
        "computeGeneGSProb",
        "computeGeneGSProb,CogapsResult-method"
      ]
    },
    {
      "page": "findConsensusMatrix",
      "title": "find the consensus pattern matrix across all subsets",
      "topics": [
        "findConsensusMatrix"
      ]
    },
    {
      "page": "fromCSV-methods",
      "title": "read CoGAPS Result object from a directory with a set of csvs see toCSV",
      "topics": [
        "fromCSV",
        "fromCSV,character-method"
      ]
    },
    {
      "page": "getAmplitudeMatrix-methods",
      "title": "return Amplitude matrix from CogapsResult object",
      "topics": [
        "getAmplitudeMatrix",
        "getAmplitudeMatrix,CogapsResult-method"
      ]
    },
    {
      "page": "getClusteredPatterns-methods",
      "title": "return clustered patterns from set of all patterns across all subsets",
      "topics": [
        "getClusteredPatterns",
        "getClusteredPatterns,CogapsResult-method"
      ]
    },
    {
      "page": "getCorrelationToMeanPattern-methods",
      "title": "return correlation between each pattern and the cluster mean",
      "topics": [
        "getCorrelationToMeanPattern",
        "getCorrelationToMeanPattern,CogapsResult-method"
      ]
    },
    {
      "page": "getFeatureLoadings-methods",
      "title": "return featureLoadings matrix from CogapsResult object",
      "topics": [
        "getFeatureLoadings",
        "getFeatureLoadings,CogapsResult-method"
      ]
    },
    {
      "page": "getMeanChiSq-methods",
      "title": "return chi-sq of final matrices",
      "topics": [
        "getMeanChiSq",
        "getMeanChiSq,CogapsResult-method"
      ]
    },
    {
      "page": "getOriginalParameters-methods",
      "title": "return original parameters used to generate this result",
      "topics": [
        "getOriginalParameters",
        "getOriginalParameters,CogapsResult-method"
      ]
    },
    {
      "page": "getParam-methods",
      "title": "get the value of a parameter",
      "topics": [
        "getParam",
        "getParam,CogapsParams-method"
      ]
    },
    {
      "page": "getPatternGeneSet-methods",
      "title": "generate statistics associating patterns with gene sets",
      "topics": [
        "getPatternGeneSet",
        "getPatternGeneSet,CogapsResult,list,character-method"
      ]
    },
    {
      "page": "getPatternMatrix-methods",
      "title": "return pattern matrix from CogapsResult object",
      "topics": [
        "getPatternMatrix",
        "getPatternMatrix,CogapsResult-method"
      ]
    },
    {
      "page": "getRetinaSubset",
      "title": "get specified number of retina subsets",
      "topics": [
        "getRetinaSubset"
      ]
    },
    {
      "page": "getSampleFactors-methods",
      "title": "return sampleFactors matrix from CogapsResult object",
      "topics": [
        "getSampleFactors",
        "getSampleFactors,CogapsResult-method"
      ]
    },
    {
      "page": "getSubsets-methods",
      "title": "return the names of the genes (samples) in each subset",
      "topics": [
        "getSubsets",
        "getSubsets,CogapsResult-method"
      ]
    },
    {
      "page": "getUnmatchedPatterns-methods",
      "title": "return unmatched patterns from each subset",
      "topics": [
        "getUnmatchedPatterns",
        "getUnmatchedPatterns,CogapsResult-method"
      ]
    },
    {
      "page": "getVersion-methods",
      "title": "return version number used to generate this result",
      "topics": [
        "getVersion",
        "getVersion,CogapsResult-method"
      ]
    },
    {
      "page": "GIST.data_frame",
      "title": "GIST gene expression data from Ochs et al. (2009)",
      "topics": [
        "GIST.data_frame"
      ]
    },
    {
      "page": "GIST.matrix",
      "title": "GIST gene expression data from Ochs et al. (2009)",
      "topics": [
        "GIST.matrix"
      ]
    },
    {
      "page": "GIST.result",
      "title": "CoGAPS result from running on GIST dataset",
      "topics": [
        "GIST.result"
      ]
    },
    {
      "page": "GIST.uncertainty",
      "title": "GIST gene expression uncertainty matrix from Ochs et al. (2009)",
      "topics": [
        "GIST.uncertainty"
      ]
    },
    {
      "page": "GWCoGAPS",
      "title": "Genome Wide CoGAPS",
      "topics": [
        "GWCoGAPS"
      ]
    },
    {
      "page": "initialize-CogapsParams-method",
      "title": "constructor for CogapsParams",
      "topics": [
        "initialize,CogapsParams-method"
      ]
    },
    {
      "page": "initialize-CogapsResult-method",
      "title": "Constructor for CogapsResult",
      "topics": [
        "initialize,CogapsResult-method"
      ]
    },
    {
      "page": "MANOVA-methods",
      "title": "MANOVA statistical test for patterns between sample groups",
      "topics": [
        "MANOVA",
        "MANOVA,matrix,CogapsResult-method"
      ]
    },
    {
      "page": "modsimdata",
      "title": "Toy example to run CoGAPS on.",
      "topics": [
        "modsimdata"
      ]
    },
    {
      "page": "modsimresult",
      "title": "Result of applying CoGAPS on the Toy example.",
      "topics": [
        "modsimresult"
      ]
    },
    {
      "page": "patternMarkers-methods",
      "title": "compute pattern markers statistic",
      "topics": [
        "patternMarkers",
        "patternMarkers,CogapsResult-method"
      ]
    },
    {
      "page": "plotPatternGeneSet-methods",
      "title": "generate a barchart of most significant hallmark sets for a pattern",
      "topics": [
        "plotPatternGeneSet",
        "plotPatternGeneSet,list,numeric,numeric-method"
      ]
    },
    {
      "page": "plotPatternMarkers-methods",
      "title": "heatmap of original data clustered by pattern markers statistic",
      "topics": [
        "plotPatternMarkers"
      ]
    },
    {
      "page": "plotResiduals-methods",
      "title": "plot of residuals",
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      "page": "reconstructGene-methods",
      "title": "reconstruct gene",
      "topics": [
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    },
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      "page": "scCoGAPS",
      "title": "Single Cell CoGAPS",
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      "page": "setAnnotationWeights-methods",
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      "topics": [
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      "title": "save CoGAPS Result object as a set of csvs to directory see fromCSV",
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      "source": "CoGAPS.Rmd",
      "filename": "CoGAPS.html",
      "title": "CoGAPS - Coordinated Gene Association in Pattern Sets",
      "author": "Jeanette Johnson, Ashley Tsang, Thomas Sherman, Genevieve Stein-O'Brien, Hyejune Limb, Elana Fertig",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Vignette Version",
        "Introduction",
        "Software Setup",
        "Running CoGAPS on Simulated Toy Data",
        "Analyzing the Toy Data CoGAPS result",
        "Single-cell CoGAPS",
        "Analyzing the CoGAPS result",
        "Load CoGAPS pattern information into Seurat object",
        "Plot patterns on an embedding",
        "Pattern Markers",
        "Marker assignment methods",
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        "Example",
        "Pattern GSEA",
        "Citing CoGAPS",
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      "created": "2018-08-02 19:13:19",
      "modified": "2025-03-12 12:54:01",
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