{
  "_id": "6ae660739ceaa78f20098bef",
  "Package": "cpvSNP",
  "Type": "Package",
  "Title": "Gene set analysis methods for SNP association p-values that lie\nin genes in given gene sets",
  "Version": "1.45.0",
  "Date": "2021-11-20",
  "Author": "Caitlin McHugh, Jessica Larson, and Jason Hackney",
  "Maintainer": "Caitlin McHugh <mchughc@uw.edu>",
  "Description": "Gene set analysis methods exist to combine SNP-level\nassociation p-values into gene sets, calculating a single\nassociation p-value for each gene set. This package implements\ntwo such methods that require only the calculated SNP p-values,\nthe gene set(s) of interest, and a correlation matrix (if\ndesired). One method (GLOSSI) requires independent SNPs and the\nother (VEGAS) can take into account correlation (LD) among the\nSNPs. Built-in plotting functions are available to help users\nvisualize results.",
  "License": "Artistic-2.0",
  "biocViews": "Genetics, StatisticalMethod, Pathways, GeneSetEnrichment,\nGenomicVariation",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:40:17 UTC",
  "RemoteUrl": "https://github.com/bioc/cpvSNP",
  "RemoteRef": "HEAD",
  "RemoteSha": "94067ad04b1aafb885f930b01952389f8805beea",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-31 21:26:37 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "cpvSNP_1.45.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/33e12015f1d6e7be0e7c3fcaea9feb79a9e9faec7706316f7c445b3ab289c804",
  "_filesize": 2260200,
  "_sha256": "33e12015f1d6e7be0e7c3fcaea9feb79a9e9faec7706316f7c445b3ab289c804",
  "_expires": "2027-02-08T21:41:04.000Z",
  "_created": "2026-10-31T21:26:37.000Z",
  "_published": "2026-10-31T21:41:06.846Z",
  "_upstream": "https://github.com/bioc/cpvSNP",
  "_status": "success",
  "_maintainer": {
    "name": "Caitlin McHugh",
    "email": "mchughc@uw.edu",
    "login": "mchughc",
    "description": "",
    "uuid": 6343156
  },
  "_jobs": [
    {
      "job": 124662533160,
      "time": 226,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "13058144623"
    },
    {
      "job": 124662533138,
      "time": 420,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13058930351"
    },
    {
      "job": 124662533065,
      "time": 454,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "13058800521"
    },
    {
      "job": 124662533127,
      "time": 226,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13058363445"
    },
    {
      "job": 124662533099,
      "time": 170,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13058144523"
    },
    {
      "job": 124661229821,
      "time": 337,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13057784968"
    },
    {
      "job": 124662533111,
      "time": 158,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13058560570"
    },
    {
      "job": 124662533122,
      "time": 318,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13058950626"
    },
    {
      "job": 124662533187,
      "time": 233,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13058485934"
    },
    {
      "job": 124662533150,
      "time": 290,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13058545821"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 7,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41243201621",
  "_commit": {
    "id": "94067ad04b1aafb885f930b01952389f8805beea",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380017
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "GenomicFeatures",
      "role": "Depends"
    },
    {
      "package": "GSEABase",
      "version": ">= 1.24.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "corpcor",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "ReportingTools",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.45.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.44.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "genetics",
    "statisticalmethod",
    "pathways",
    "genesetenrichment",
    "genomicvariation"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 481,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 644,
    "source": "https://www.bioconductor.org/packages/stats/bioc/cpvSNP"
  },
  "_searchresults": 9,
  "_abi": {
    "exports": [
      {
        "key": "cpvSNP::GLOSSIResult",
        "hash": "15244998687c1e48"
      },
      {
        "key": "cpvSNP::GLOSSIResultCollection",
        "hash": "3834b47fc66776ac"
      },
      {
        "key": "cpvSNP::GeneSetResult",
        "hash": "b2f68691bfbccfc4"
      },
      {
        "key": "cpvSNP::GeneSetResultCollection",
        "hash": "222c86afd3ea2bd7"
      },
      {
        "key": "cpvSNP::VEGASResult",
        "hash": "fc1ea17a5c029cb7"
      },
      {
        "key": "cpvSNP::VEGASResultCollection",
        "hash": "1b49adb975a313da"
      }
    ],
    "imports": []
  },
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/cpvSNP.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "assocPvalBySetPlot",
    "createArrayData",
    "degreesOfFreedom",
    "geneSetName",
    "geneToSNPList",
    "glossi",
    "glossiMarginal",
    "plotPvals",
    "pValue",
    "simulate_chisq",
    "simulatedStats",
    "statistic",
    "vegas",
    "vegasMarginal"
  ],
  "_datasets": [
    {
      "name": "geneSetAnalysis",
      "title": "Data to run gene set analysis methods",
      "object": "geneSetAnalysis",
      "file": "geneSetAnalysis.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "assocPvalBySetPlot",
      "title": "Create a Density Plot of P-Values, Highlighting SNPs Within a Gene Set",
      "topics": [
        "assocPvalBySetPlot"
      ]
    },
    {
      "page": "createArrayData",
      "title": "Create a GRanges Object for a GWAS data.frame",
      "topics": [
        "createArrayData"
      ]
    },
    {
      "page": "degreesOfFreedom-method",
      "title": "~~ Methods for Function 'degreesOfFreedom' ~~",
      "topics": [
        "degreesOfFreedom",
        "degreesOfFreedom,GeneSetResult-method",
        "degreesOfFreedom,GeneSetResultCollection-method",
        "degreesOfFreedom,GLOSSIResult-method",
        "degreesOfFreedom,GLOSSIResultCollection-method",
        "degreesOfFreedom,VEGASResult-method",
        "degreesOfFreedom,VEGASResultCollection-method",
        "degreesOfFreedom-methods"
      ]
    },
    {
      "page": "exampleArrayData",
      "title": "SNP Array Data to Use for Gene Set Analysis",
      "topics": [
        "exampleArrayData"
      ]
    },
    {
      "page": "geneSetAnalysis",
      "title": "Data to run gene set analysis methods",
      "topics": [
        "geneSetAnalysis"
      ]
    },
    {
      "page": "geneSetName-methods",
      "title": "~~ Methods for Function 'geneSetName' ~~",
      "topics": [
        "geneSetName",
        "geneSetName,GeneSetResult-method",
        "geneSetName,GeneSetResultCollection-method",
        "geneSetName,GLOSSIResult-method",
        "geneSetName,GLOSSIResultCollection-method",
        "geneSetName,VEGASResult-method",
        "geneSetName,VEGASResultCollection-method",
        "geneSetName-methods"
      ]
    },
    {
      "page": "GeneSetResult-class",
      "title": "Class '\"GeneSetResult\"'",
      "topics": [
        "GeneSetResult-class"
      ]
    },
    {
      "page": "GeneSetResultCollection-class",
      "title": "Class '\"GeneSetResultCollection\"'",
      "topics": [
        "GeneSetResultCollection-class"
      ]
    },
    {
      "page": "geneSets",
      "title": "Gene Set Collection object",
      "topics": [
        "geneSets"
      ]
    },
    {
      "page": "geneToSNPList",
      "title": "Translate a List of Gene Ids to Their Corresponding SNP Ids",
      "topics": [
        "geneToSNPList"
      ]
    },
    {
      "page": "glossi",
      "title": "Calculate a Chi-squared Statistic and P-Value for Independent Items of a Set Using the GLOSSI Method",
      "topics": [
        "glossi"
      ]
    },
    {
      "page": "glossiMarginal",
      "title": "Calculate a Chi-squared Statistic and P-Value for Items in a Set",
      "topics": [
        "glossiMarginal"
      ]
    },
    {
      "page": "GLOSSIResult-class",
      "title": "Class '\"GLOSSIResult\"'",
      "topics": [
        "GLOSSIResult-class"
      ]
    },
    {
      "page": "GLOSSIResultCollection-class",
      "title": "Class '\"GLOSSIResultCollection\"'",
      "topics": [
        "GLOSSIResultCollection-class"
      ]
    },
    {
      "page": "plotPvals",
      "title": "Create a Plot of P-Values Against Number of SNPs per Set for All Sets in a Collection",
      "topics": [
        "plotPvals"
      ]
    },
    {
      "page": "pValue-method",
      "title": "~~ Methods for Function 'pValue' ~~",
      "topics": [
        "pValue",
        "pValue,GeneSetResult-method",
        "pValue,GeneSetResultCollection-method",
        "pValue,GLOSSIResult-method",
        "pValue,GLOSSIResultCollection-method",
        "pValue,VEGASResult-method",
        "pValue,VEGASResultCollection-method",
        "pValue-methods"
      ]
    },
    {
      "page": "simulate_chisq",
      "title": "Simulate a Chi-squared Statistic from a Distribution with a Specified Correlation Structure",
      "topics": [
        "simulate_chisq"
      ]
    },
    {
      "page": "simulatedStats-method",
      "title": "~~ Methods for Function 'simulatedStats' ~~",
      "topics": [
        "simulatedStats",
        "simulatedStats,VEGASResult-method",
        "simulatedStats,VEGASResultCollection-method",
        "simulatedStats-methods"
      ]
    },
    {
      "page": "statistic-methods",
      "title": "~~ Methods for Function 'statistic' ~~",
      "topics": [
        "statistic",
        "statistic,GeneSetResult-method",
        "statistic,GeneSetResultCollection-method",
        "statistic,GLOSSIResult-method",
        "statistic,GLOSSIResultCollection-method",
        "statistic,VEGASResult-method",
        "statistic,VEGASResultCollection-method",
        "statistic-methods"
      ]
    },
    {
      "page": "show-methods",
      "title": "~~ Methods for Function 'show' in Package 'base' ~~",
      "topics": [
        "show",
        "show,GLOSSIResult-method",
        "show,VEGASResult-method",
        "show-methods"
      ]
    },
    {
      "page": "vegas",
      "title": "Calculate the P-Value for a Set Using the VEGAS Method",
      "topics": [
        "vegas"
      ]
    },
    {
      "page": "vegasMarginal",
      "title": "Calculate the P-Value for a Set Using the VEGAS Method",
      "topics": [
        "vegasMarginal"
      ]
    },
    {
      "page": "VEGASResult-class",
      "title": "Class '\"VEGASResult\"'",
      "topics": [
        "VEGASResult-class"
      ]
    },
    {
      "page": "VEGASResultCollection-class",
      "title": "Class '\"VEGASResultCollection\"'",
      "topics": [
        "VEGASResultCollection-class"
      ]
    }
  ],
  "_rundeps": [
    "annotate",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "corpcor",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "farver",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "graph",
    "GSEABase",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lifecycle",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "plyr",
    "png",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "sys",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "cpvSNP.Rnw",
      "filename": "cpvSNP.pdf",
      "title": "Running gene set analyses with the \"cpvSNP\" package",
      "engine": "utils::Sweave",
      "headings": [
        "1 Introduction ",
        "2 Example workflow for cpvSNP",
        "3 Methods in brief",
        "4 Session Info",
        "5 References"
      ],
      "created": "2014-11-24 22:55:55",
      "modified": "2015-04-09 20:24:48",
      "commits": 2
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "cpvsnp",
  "_universes": [
    "bioc",
    "mchughc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.45.0",
      "date": "2026-10-31T21:31:40.000Z",
      "distro": "resolute",
      "commit": "94067ad04b1aafb885f930b01952389f8805beea",
      "fileid": "https://r2.ropensci.org/08ea1531b4e5db8de411f1a02712248f1427accdf3b6dcc34e7ed29275f3f164",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41243201621"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.45.0",
      "date": "2026-10-31T21:32:30.000Z",
      "distro": "resolute",
      "commit": "94067ad04b1aafb885f930b01952389f8805beea",
      "fileid": "https://r2.ropensci.org/1bc72a27680658669c65ed9cbb615f4e12bb1630dfbac594a6f2a446705eea58",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41243201621"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.45.0",
      "date": "2026-10-31T21:29:25.000Z",
      "commit": "94067ad04b1aafb885f930b01952389f8805beea",
      "fileid": "https://r2.ropensci.org/95d9538d8b51622199821546200b7884bab91f73c6fb8f126e423d75e4a1f13f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41243201621"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.45.0",
      "date": "2026-10-31T21:28:55.000Z",
      "commit": "94067ad04b1aafb885f930b01952389f8805beea",
      "fileid": "https://r2.ropensci.org/4a36967be1afbce59912316eae0d20eba05709f883ae0a7baca6cdb582b5fdcd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41243201621"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.45.0",
      "date": "2026-10-31T21:29:47.000Z",
      "commit": "94067ad04b1aafb885f930b01952389f8805beea",
      "fileid": "https://r2.ropensci.org/56c8f7108862bf01d40463c00ad779105a10ee6f6b3e53dde0db705a685982d2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41243201621"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-10-31T21:29:08.000Z",
      "commit": "94067ad04b1aafb885f930b01952389f8805beea",
      "fileid": "https://r2.ropensci.org/0fa681ee8ea3141b3e790a24a8f1787772895be55061f087e32c608418b2f538",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41243201621"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-10-31T21:28:41.000Z",
      "commit": "94067ad04b1aafb885f930b01952389f8805beea",
      "fileid": "https://r2.ropensci.org/95f3a2a06a7dbeb22e27322bd50adf1b18fdba51ca65e07ee9162c735a0db070",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41243201621"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-10-31T21:28:59.000Z",
      "commit": "94067ad04b1aafb885f930b01952389f8805beea",
      "fileid": "https://r2.ropensci.org/882507ee25fb6df992f835ee35d688596e44486285bed65917266890c601606b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41243201621"
    }
  ]
}