{
  "_id": "6a4798102f27a93436c0f9db",
  "Package": "aSPU",
  "Version": "1.50",
  "Date": "2021-6-28",
  "Title": "Adaptive Sum of Powered Score Test",
  "Description": "R codes for the (adaptive) Sum of Powered Score ('SPU' and\n'aSPU') tests, inverse variance weighted Sum of Powered score\n('SPUw' and 'aSPUw') tests and gene-based and some pathway\nbased association tests (Pathway based Sum of Powered Score\ntests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test,\n'GEEaSPU' test for multiple traits - single 'SNP' (single\nnucleotide polymorphism) association in generalized estimation\nequations, 'MTaSPUs' test for multiple traits - single 'SNP'\nassociation with Genome Wide Association Studies ('GWAS')\nsummary statistics, Gene-based Association Test that uses an\nextended 'Simes' procedure ('GATES'), Hybrid Set-based Test\n('HYST') and extended version of 'GATES' test for pathway-based\nassociation testing ('GATES-Simes'). ). The tests can be used\nwith genetic and other data sets with covariates. The response\nvariable is binary or quantitative. Summary; (1) Single\ntrait-'SNP' set association with individual-level data ('aSPU',\n'aSPUw', 'aSPUr'), (2) Single trait-'SNP' set association with\nsummary statistics ('aSPUs'), (3) Single trait-pathway\nassociation with individual-level data ('aSPUpath'), (4) Single\ntrait-pathway association with summary statistics\n('aSPUsPath'), (5) Multiple traits-single 'SNP' association\nwith individual-level data ('GEEaSPU'), (6) Multiple traits-\nsingle 'SNP' association with summary statistics ('MTaSPUs'),\n(7) Multiple traits-'SNP' set association with summary\nstatistics('MTaSPUsSet'), (8) Multiple traits-pathway\nassociation with summary statistics('MTaSPUsSetPath').",
  "Author": "Il-Youp Kwak and others (See Author(s) in each function manual)",
  "Maintainer": "Il-Youp Kwak <ikwak2@cau.ac.kr>",
  "VignetteBuilder": "knitr",
  "License": "GPL-3",
  "URL": "https://github.com/ikwak2/aSPU",
  "RoxygenNote": "7.1.0",
  "Repository": "https://ikwak2.r-universe.dev",
  "Date/Publication": "2021-06-28 16:38:24 UTC",
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      "package": "gee",
      "role": "Depends"
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      "package": "MASS",
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      "package": "mvtnorm",
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/aSPU"
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  "_mentions": 11,
  "_devurl": "https://github.com/ikwak2/aspu",
  "_searchresults": 46,
  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/ikwak2/aspu",
  "_realowner": "ikwak2",
  "_cranurl": true,
  "_releases": [
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      "version": "1.33",
      "date": "2015-05-27"
    },
    {
      "version": "1.35",
      "date": "2015-06-04"
    },
    {
      "version": "1.36",
      "date": "2015-07-28"
    },
    {
      "version": "1.37",
      "date": "2015-08-03"
    },
    {
      "version": "1.38",
      "date": "2015-10-26"
    },
    {
      "version": "1.39",
      "date": "2015-12-22"
    },
    {
      "version": "1.40",
      "date": "2016-02-18"
    },
    {
      "version": "1.41",
      "date": "2016-03-21"
    },
    {
      "version": "1.42",
      "date": "2016-05-02"
    },
    {
      "version": "1.43",
      "date": "2016-09-15"
    },
    {
      "version": "1.44",
      "date": "2016-09-22"
    },
    {
      "version": "1.45",
      "date": "2016-10-11"
    },
    {
      "version": "1.46",
      "date": "2016-11-08"
    },
    {
      "version": "1.47",
      "date": "2017-05-21"
    },
    {
      "version": "1.48",
      "date": "2017-06-24"
    },
    {
      "version": "1.49",
      "date": "2020-05-13"
    },
    {
      "version": "1.50",
      "date": "2021-06-28"
    }
  ],
  "_exports": [
    "aSPU",
    "aSPUd",
    "aSPUpath",
    "aSPUpath2",
    "aSPUr",
    "aSPUs",
    "aSPUsD",
    "aSPUsPath",
    "aSPUsPath2",
    "aSPUw",
    "estcov",
    "GATES2",
    "GatesSimes",
    "GEEaSPU",
    "getlogitp",
    "Hyst",
    "minP",
    "MTaSPUs",
    "MTaSPUsSet",
    "MTaSPUsSetPath",
    "MTaSPUsSetScore",
    "plotPmat",
    "pruneSNP",
    "simPathAR1Snp"
  ],
  "_datasets": [
    {
      "name": "exdat",
      "title": "An example data set",
      "object": "exdat",
      "file": "exdat.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "kegg9",
      "title": "A subset of coronary artery disease (CAD) data",
      "object": "kegg9",
      "file": "kegg9.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "SAMD11",
      "title": "An example data for MTaSPUsSet test",
      "object": "SAMD11",
      "file": "SAMD11.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "someGs",
      "title": "An example data for MTaSPUsSet test",
      "object": "someGs",
      "file": "someGs.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "aSPU",
      "title": "Sum of Powered Score (SPU) tests and adaptive SPU (aSPU) test for single trait - SNP set association.",
      "topics": [
        "aSPU"
      ]
    },
    {
      "page": "aSPUd",
      "title": "Adaptive Sum of powered score (SPU) tests (SPU and aSPU) based on asymptotic distribution.",
      "topics": [
        "aSPUd"
      ]
    },
    {
      "page": "aSPUpath",
      "title": "Pathway based Sum of Powered Score tests (SPUpath) and adaptive SPUpath (aSPUpath) test for single trait - pathway association.",
      "topics": [
        "aSPUpath"
      ]
    },
    {
      "page": "aSPUpath2",
      "title": "Pathway based Sum of Powered Score tests (SPUpath) and adaptive SPUpath (aSPUpath) test for single trait - pathway association. (vector version, fast when n is large)",
      "topics": [
        "aSPUpath2"
      ]
    },
    {
      "page": "aSPUr",
      "title": "Robust Sum of powered score (SPU) tests and aSPU test for a quantitative trait",
      "topics": [
        "aSPUr"
      ]
    },
    {
      "page": "aSPUs",
      "title": "Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs) test for single trait - SNP set association with GWAS summary statistics.",
      "topics": [
        "aSPUs"
      ]
    },
    {
      "page": "aSPUsD",
      "title": "Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs) test for single trait - SNP set association with GWAS summary statistics (distribution based).",
      "topics": [
        "aSPUsD"
      ]
    },
    {
      "page": "aSPUsPath",
      "title": "Pathway based Sum of Powered Score tests (SPUsPath) and adaptive SPUpath (aSPUsPath) test for single trait - pathway association with GWAS summary statistics.",
      "topics": [
        "aSPUsPath"
      ]
    },
    {
      "page": "aSPUsPath2",
      "title": "Pathway based Sum of Powered Score tests (SPUsPath) and adaptive SPUpath (aSPUsPath) test for single trait - pathway association with GWAS summary statistics. (vector version, fast when n is large)",
      "topics": [
        "aSPUsPath2"
      ]
    },
    {
      "page": "aSPUw",
      "title": "Inverse variance weighted Sum of Powered Score tests (SPUw) and adaptive SPUw (aSPUw) test for single trait - SNP set association.",
      "topics": [
        "aSPUw"
      ]
    },
    {
      "page": "estcov",
      "title": "estcov",
      "topics": [
        "estcov"
      ]
    },
    {
      "page": "exdat",
      "title": "An example data set",
      "topics": [
        "exdat"
      ]
    },
    {
      "page": "GATES2",
      "title": "Gene-based Association Test that uses an extended Simes procedure (GATES) for single trait - SNP set association",
      "topics": [
        "GATES2"
      ]
    },
    {
      "page": "GatesSimes",
      "title": "GATES-Simes test for single trait - pathway association.",
      "topics": [
        "GatesSimes"
      ]
    },
    {
      "page": "GEEaSPU",
      "title": "The SPU and aSPU tests for multiple traits - single SNP association in generalized estimating equations.",
      "topics": [
        "GEEaSPU"
      ]
    },
    {
      "page": "getlogitp",
      "title": "Get the p-values of the multiple SNPs based on the Wald test in a logistic regresion model.",
      "topics": [
        "getlogitp"
      ]
    },
    {
      "page": "Hyst",
      "title": "HYST (Hybrid Set-based Test) for single trait - pathway association",
      "topics": [
        "Hyst"
      ]
    },
    {
      "page": "kegg9",
      "title": "A subset of coronary artery disease (CAD) data",
      "topics": [
        "kegg9"
      ]
    },
    {
      "page": "minP",
      "title": "minP test.",
      "topics": [
        "minP"
      ]
    },
    {
      "page": "MTaSPUs",
      "title": "The SPU and aSPU tests for multiple traits - single SNP association with GWAS summary statistics.",
      "topics": [
        "MTaSPUs"
      ]
    },
    {
      "page": "MTaSPUsSet",
      "title": "gene-Multitrait Sum of Powered Score (MTSPUsSet) tests and adaptive MTSPUsSet (MTaSPUsSet) test for multi trait - SNP set association with GWAS summary statistics.",
      "topics": [
        "MTaSPUsSet"
      ]
    },
    {
      "page": "MTaSPUsSetPath",
      "title": "Multitraits - Pathway based Sum of Powered Score tests (MTSPUsSetPath) and adaptive MTSPUsSetpath (MTaSPUsSetPath) test for multi trait - pathway association with GWAS summary statistics.",
      "topics": [
        "MTaSPUsSetPath"
      ]
    },
    {
      "page": "MTaSPUsSetScore",
      "title": "gene-Multitrait Sum of Powered Score (MTSPUsSetScore) tests and adaptive MTSPUsSet (MTaSPUsSet) test for multi trait - SNP set association with GWAS summary statistics. (Score version added)",
      "topics": [
        "MTaSPUsSetScore"
      ]
    },
    {
      "page": "plotPmat",
      "title": "Image plot of P-value matrix.",
      "topics": [
        "plotPmat"
      ]
    },
    {
      "page": "pruneSNP",
      "title": "Prune SNPs (related to aSPUs, aSPUsPath, MTaSPUsSet)",
      "topics": [
        "pruneSNP"
      ]
    },
    {
      "page": "SAMD11",
      "title": "An example data for MTaSPUsSet test",
      "topics": [
        "SAMD11"
      ]
    },
    {
      "page": "simPathAR1Snp",
      "title": "Simulating a pathway with multiple SNPs.",
      "topics": [
        "simPathAR1Snp"
      ]
    },
    {
      "page": "someGs",
      "title": "An example data for MTaSPUsSet test",
      "topics": [
        "someGs"
      ]
    }
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  "_readme": "https://github.com/ikwak2/aspu/raw/HEAD/README.md",
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      "engine": "knitr::rmarkdown",
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        "Data",
        "Use of aSPUs function",
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      "author": "Il-Youp Kwak",
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