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  "Package": "SKAT",
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  "Title": "SNP-Set (Sequence) Kernel Association Test",
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  "Date": "2025-08-06",
  "Author": "Seunggeun (Shawn) Lee and Zhangchen Zhao, with contributions\nfrom Larisa Miropolsky and Michael Wu",
  "Maintainer": "Seunggeun (Shawn) Lee <lee7801@snu.ac.kr>",
  "Description": "Functions for kernel-regression-based association tests\nincluding Burden test, SKAT and SKAT-O. These methods aggregate\nindividual SNP score statistics in a SNP set and efficiently\ncompute SNP-set level p-values.",
  "License": "GPL (>= 2)",
  "Repository": "https://leelabsg.r-universe.dev",
  "Date/Publication": "2025-08-07 00:50:43 UTC",
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  "_topics": [
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    "cpp"
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    "manual.pdf"
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    {
      "version": "1.0.1",
      "date": "2014-11-04"
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    {
      "version": "1.0.7",
      "date": "2015-04-19"
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    {
      "version": "1.1.2",
      "date": "2015-09-08"
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    {
      "version": "1.3.0",
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      "version": "1.3.2.1",
      "date": "2017-08-03"
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    {
      "version": "2.2.4",
      "date": "2022-03-29"
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    {
      "version": "2.2.5",
      "date": "2023-01-15"
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  ],
  "_exports": [
    "Close_SSD",
    "Generate_SSD_SetID",
    "Get_Davies_PVal",
    "Get_EffectiveNumberTest",
    "Get_Genotypes_SSD",
    "Get_Genotypes_SSD_Sparse",
    "Get_Lambda",
    "Get_Liu_PVal",
    "Get_Logistic_Weights",
    "Get_Logistic_Weights_MAF",
    "Get_RequiredSampleSize",
    "Get_Resampling_Pvalue",
    "Get_Resampling_Pvalue_1",
    "Open_SSD",
    "Power_Continuous",
    "Power_Continuous_R",
    "Power_Logistic",
    "Power_Logistic_R",
    "QQPlot_Adj",
    "Read_Plink_FAM",
    "Read_Plink_FAM_Cov",
    "Read_SNP_WeightFile",
    "Resampling_FWER",
    "Resampling_FWER_1",
    "SKAT",
    "SKAT_Check_Method",
    "SKAT_ChrX",
    "SKAT_ChrY",
    "SKAT_CommonRare",
    "SKAT_CommonRare_Robust",
    "SKAT_CommonRare_Robust.SSD.All",
    "SKAT_CommonRare_Robust.SSD.OneSet",
    "SKAT_CommonRare_Robust.SSD.OneSet_SetIndex",
    "SKAT_CommonRare.SSD.All",
    "SKAT_CommonRare.SSD.OneSet",
    "SKAT_CommonRare.SSD.OneSet_SetIndex",
    "SKAT_META_Optimal",
    "SKAT_NULL_emmaX",
    "SKAT_Null_Model",
    "SKAT_Null_Model_ChrX",
    "SKAT_Null_Model_MomentAdjust",
    "SKAT_Optimal_Each_Q",
    "SKAT_Optimal_PValue_Davies",
    "SKAT_Optimal_PValue_Liu",
    "SKAT.SSD.All",
    "SKAT.SSD.OneSet",
    "SKAT.SSD.OneSet_SetIndex",
    "SKATBinary",
    "SKATBinary_Robust",
    "SKATBinary_Robust.SSD.All",
    "SKATBinary_Robust.SSD.OneSet",
    "SKATBinary_Robust.SSD.OneSet_SetIndex",
    "SKATBinary_Single",
    "SKATBinary.SSD.All",
    "SKATBinary.SSD.OneSet",
    "SKATBinary.SSD.OneSet_SetIndex"
  ],
  "_datasets": [
    {
      "name": "SKAT.example",
      "title": "Example data for SKAT",
      "object": "SKAT.example",
      "file": "SKAT.example.ChrX.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "SKAT.example.ChrX",
      "title": "Example data for SKAT",
      "object": "SKAT.example.ChrX",
      "file": "SKAT.example.ChrX.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "SKAT.fam.example",
      "title": "Example data for SKAT_NULL_emmaX",
      "object": "SKAT.fam.example",
      "file": "SKAT.fam.example.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "SKAT.haplotypes",
      "title": "Haplotype dataset for power calculation",
      "object": "SKAT.haplotypes",
      "file": "SKAT.haplotypes.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "SKATBinary.example",
      "title": "Example data for SKAT",
      "object": "SKATBinary.example",
      "file": "SKATBinary.example.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Close_SSD",
      "title": "Close SNP set data file (SSD)",
      "topics": [
        "Close_SSD"
      ]
    },
    {
      "page": "Generate_SSD_SetID",
      "title": "Generate SNP set data file (SSD)",
      "topics": [
        "Generate_SSD_SetID"
      ]
    },
    {
      "page": "Get_ENT",
      "title": "Estimate the effective number of tests for Bonferroni correction",
      "topics": [
        "Get_EffectiveNumberTest"
      ]
    },
    {
      "page": "Get_Genotypes_SSD",
      "title": "Get Genotype data from SSD file",
      "topics": [
        "Get_Genotypes_SSD",
        "Get_Genotypes_SSD_Sparse"
      ]
    },
    {
      "page": "Get_Logistic_Weights",
      "title": "Get the logistic weight",
      "topics": [
        "Get_Logistic_Weights",
        "Get_Logistic_Weights_MAF"
      ]
    },
    {
      "page": "Get_RequiredSampleSize",
      "title": "Get the required sample size to achieve the given power",
      "topics": [
        "Get_RequiredSampleSize"
      ]
    },
    {
      "page": "Get_Resampling_Pvalue",
      "title": "Compute a resampling p-value",
      "topics": [
        "Get_Resampling_Pvalue",
        "Get_Resampling_Pvalue_1"
      ]
    },
    {
      "page": "Open_SSD",
      "title": "Open SNP set data file (SSD)",
      "topics": [
        "Open_SSD"
      ]
    },
    {
      "page": "Power_Continuous",
      "title": "Power calculation, continuous traits",
      "topics": [
        "Power_Continuous",
        "Power_Continuous_R"
      ]
    },
    {
      "page": "Power_Logistic",
      "title": "Power calculation, Dichotomous traits",
      "topics": [
        "Power_Logistic",
        "Power_Logistic_R"
      ]
    },
    {
      "page": "QQPlot_Adj",
      "title": "Adjusted QQ plot",
      "topics": [
        "QQPlot_Adj"
      ]
    },
    {
      "page": "Read_Plink_FAM",
      "title": "Read Plink FAM and covariates files",
      "topics": [
        "Read_Plink_FAM",
        "Read_Plink_FAM_Cov"
      ]
    },
    {
      "page": "Read_SNP_WeightFile",
      "title": "Read a file with custom weights",
      "topics": [
        "Read_SNP_WeightFile"
      ]
    },
    {
      "page": "Resampling_FWER",
      "title": "Obtain significant SNP sets after controlling family wise error rate (FWER)",
      "topics": [
        "Resampling_FWER",
        "Resampling_FWER_1"
      ]
    },
    {
      "page": "SKAT",
      "title": "SNP-set (Sequence) Kernel Association Test",
      "topics": [
        "SKAT",
        "SKAT.SSD.OneSet",
        "SKAT.SSD.OneSet_SetIndex"
      ]
    },
    {
      "page": "SKAT_ChrX",
      "title": "SNP-set (Sequence) Kernel Association Test for X and Y chromosome variables",
      "topics": [
        "SKAT_ChrX",
        "SKAT_ChrY"
      ]
    },
    {
      "page": "SKAT_CommonRare",
      "title": "SKAT for the combined effect of common and rare variants",
      "topics": [
        "SKAT_CommonRare",
        "SKAT_CommonRare.SSD.OneSet",
        "SKAT_CommonRare.SSD.OneSet_SetIndex"
      ]
    },
    {
      "page": "SKAT_CommonRare_Robust",
      "title": "SNP set test (both common and rare variants) for binary traits with robust region-based methods",
      "topics": [
        "SKAT_CommonRare_Robust",
        "SKAT_CommonRare_Robust.SSD.OneSet",
        "SKAT_CommonRare_Robust.SSD.OneSet_SetIndex"
      ]
    },
    {
      "page": "SKAT_NULL_emmaX",
      "title": "Get parameters and residuals from the null model with incorporating the kinship structure",
      "topics": [
        "SKAT_NULL_emmaX"
      ]
    },
    {
      "page": "SKAT_Null_Model",
      "title": "Get parameters and residuals from the NULL model",
      "topics": [
        "SKAT_Null_Model",
        "SKAT_Null_Model_ChrX"
      ]
    },
    {
      "page": "SKAT_Null_Model_MomentAdjust",
      "title": "Get parameters and residuals from the NULL model for small sample adjustment",
      "topics": [
        "SKAT_Null_Model_MomentAdjust"
      ]
    },
    {
      "page": "SKAT.example",
      "title": "Example data for SKAT",
      "topics": [
        "SKAT.example"
      ]
    },
    {
      "page": "SKAT.example.ChrX",
      "title": "Example data for SKAT",
      "topics": [
        "SKAT.example.ChrX"
      ]
    },
    {
      "page": "SKAT.fam.example",
      "title": "Example data for SKAT_NULL_emmaX",
      "topics": [
        "SKAT.fam.example"
      ]
    },
    {
      "page": "SKAT.haplotypes",
      "title": "Haplotype dataset for power calculation",
      "topics": [
        "SKAT.haplotypes"
      ]
    },
    {
      "page": "SKAT.SSD.All",
      "title": "SNP-set Kernel Association Test",
      "topics": [
        "SKAT.SSD.All",
        "SKATBinary.SSD.All",
        "SKATBinary_Robust.SSD.All",
        "SKAT_CommonRare.SSD.All",
        "SKAT_CommonRare_Robust.SSD.All"
      ]
    },
    {
      "page": "SKATBinary",
      "title": "SNP set test for binary traits with asymptotic and efficient resampling methods",
      "topics": [
        "SKATBinary",
        "SKATBinary.SSD.OneSet",
        "SKATBinary.SSD.OneSet_SetIndex"
      ]
    },
    {
      "page": "SKATBinary_Robust",
      "title": "SNP set test for binary traits with robust region-based methods",
      "topics": [
        "SKATBinary_Robust",
        "SKATBinary_Robust.SSD.OneSet",
        "SKATBinary_Robust.SSD.OneSet_SetIndex"
      ]
    },
    {
      "page": "SKATBinary_Single",
      "title": "Single variant tests for binary traits with Firth and efficient resampling methods",
      "topics": [
        "SKATBinary_Single"
      ]
    },
    {
      "page": "SKATBinary.example",
      "title": "Example data for SKAT",
      "topics": [
        "SKATBinary.example"
      ]
    },
    {
      "page": "SSD_FILE_OPEN",
      "title": "Internal variables for SSD and functions for other packages",
      "topics": [
        "Get_Davies_PVal",
        "Get_Lambda",
        "Get_Liu_PVal",
        "SKAT_Check_Method",
        "SKAT_Optimal_Each_Q",
        "SKAT_Optimal_PValue_Davies",
        "SKAT_Optimal_PValue_Liu",
        "SSD_FILE_OPEN.FileName",
        "SSD_FILE_OPEN.isOpen"
      ]
    }
  ],
  "_readme": "https://github.com/leelabsg/skat/raw/HEAD/README.md",
  "_rundeps": [
    "lattice",
    "Matrix",
    "Rcpp",
    "RcppEigen",
    "RSpectra",
    "SPAtest"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
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      "source": "SKAT.Rnw",
      "filename": "SKAT.pdf",
      "title": "SKAT",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2016-08-29 18:16:53",
      "modified": "2020-12-23 07:57:12",
      "commits": 6
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  "_indexed": true,
  "_nocasepkg": "skat",
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    "leeshawn"
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