{
  "_id": "6a1ef17fb401979e7341365e",
  "Package": "CheckSumStats",
  "Title": "CheckSumStats",
  "Version": "0.0.0.9000",
  "Authors@R": "person(given = \"Philip\",\nfamily = \"Haycock\",\nrole = c(\"aut\", \"cre\"),\nemail = \"philip.haycock@bristol.ac.uk\",\ncomment = c(ORCID = \"0000-0001-5001-3350\"))",
  "Description": "CheckSumStats is an R package for checking the accuracy of\nmeta- and summary-data from genome-wide association studies\n(GWAS) prior to their use in post-GWAS applications. For\nexample, the package provides tools for checking that the\nreported effect allele and effect allele frequency columns are\ncorrect. It also checks for possible issues in the reported\neffect sizes that might introduce bias into downstream\nanalyses.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "Config/testthat/edition": "3",
  "Remotes": [
    "bioc::release/biomaRt",
    "ramiromagno/gwasrapidd"
  ],
  "Repository": "https://mrcieu.r-universe.dev",
  "Date/Publication": "2023-05-02 10:15:05 UTC",
  "RemoteUrl": "https://github.com/MRCIEU/CheckSumStats",
  "RemoteRef": "HEAD",
  "RemoteSha": "ba670767d42a9f6041b65e4a155b64a3ac096434",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-19 08:07:27 UTC",
    "User": "root"
  },
  "Author": "Philip Haycock [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5001-3350>)",
  "Maintainer": "Philip Haycock <philip.haycock@bristol.ac.uk>",
  "MD5sum": "2bcc9b48ebb741a807dbf5910b3a7345",
  "_user": "mrcieu",
  "_type": "src",
  "_file": "CheckSumStats_0.0.0.9000.tar.gz",
  "_fileid": "0716f7ec9da1a7474b823ece6e0670f9f1c25f3e325e17e08fe2b8d192228716",
  "_filesize": 1784577,
  "_sha256": "0716f7ec9da1a7474b823ece6e0670f9f1c25f3e325e17e08fe2b8d192228716",
  "_created": "2026-05-19T08:07:27.000Z",
  "_published": "2026-06-02T15:06:39.370Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79103098615,
      "time": 152,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7078138052"
    },
    {
      "job": 79103099708,
      "time": 163,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7078141013"
    },
    {
      "job": 79103100062,
      "time": 95,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7078119606"
    },
    {
      "job": 79103099476,
      "time": 114,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7078125098"
    },
    {
      "job": 79103098154,
      "time": 273,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7078087714"
    },
    {
      "job": 79103098039,
      "time": 158,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 79103099008,
      "time": 86,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7078116991"
    },
    {
      "job": 79103099879,
      "time": 88,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7078117471"
    },
    {
      "job": 79103099903,
      "time": 83,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7078115996"
    }
  ],
  "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26084386107",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/MRCIEU/CheckSumStats",
  "_commit": {
    "id": "ba670767d42a9f6041b65e4a155b64a3ac096434",
    "author": "Philip Haycock <philip.haycock@bristol.ac.uk>",
    "committer": "Philip Haycock <philip.haycock@bristol.ac.uk>",
    "message": "corrected error in zz plot function that was making point sizes too big\n",
    "time": 1683022505
  },
  "_maintainer": {
    "name": "Philip Haycock",
    "email": "philip.haycock@bristol.ac.uk",
    "login": "mightyphil2000",
    "description": "",
    "uuid": 10760254,
    "orcid": "0000-0001-5001-3350"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "gwasrapidd",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "ieugwasr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "curl",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "mrcieu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 10,
  "_contributors": [
    {
      "user": "mightyphil2000",
      "count": 193,
      "uuid": 10760254
    },
    {
      "user": "remlapmot",
      "count": 10,
      "uuid": 3777473
    }
  ],
  "_userbio": {
    "uuid": 15654827,
    "type": "organization",
    "name": "MRC Integrative Epidemiology Unit"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CheckSumStats"
  },
  "_devurl": "https://github.com/mrcieu/checksumstats",
  "_searchresults": 26,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/CheckSumStats.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "combine_plots",
    "compare_effect_to_gwascatalog",
    "compare_effect_to_gwascatalog2",
    "extract_sig_snps",
    "extract_snps",
    "find_hits_in_gwas_catalog",
    "flag_af_conflicts",
    "flag_gc_conflicts",
    "flag_gc_conflicts2",
    "format_data",
    "get_efo",
    "gwas_catalog_hits",
    "infer_ancestry",
    "make_plot_gwas_catalog",
    "make_plot_maf",
    "make_plot_pred_effect",
    "make_snplist",
    "predict_beta_sd",
    "predict_lnor_sh",
    "transform_betas",
    "zz_plot"
  ],
  "_datasets": [
    {
      "name": "ara_test_dat",
      "title": "A example dataset of genetic summary data for arachidonic acid",
      "object": "ara_test_dat",
      "class": [
        "data.frame"
      ],
      "fields": [
        "snp",
        "effect_allele",
        "other_allele",
        "effect_allele_freq",
        "beta",
        "se",
        "p",
        "n",
        "path_to_target_file"
      ],
      "rows": 436,
      "table": true,
      "tojson": true
    },
    {
      "name": "charge_top_hits",
      "title": "GWAS top hits for arachidonic acid in the CHARGE consortium",
      "object": "charge_top_hits",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "charge_top_hits_cleaned",
      "title": "GWAS top hits for arachidonic acid in the CHARGE consortium after post-GWAS cleaning",
      "object": "charge_top_hits_cleaned",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "glioma_test_dat",
      "title": "A example dataset of genetic summary data",
      "object": "glioma_test_dat",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Locus",
        "Allele1",
        "Allele2",
        "MAF",
        "Geno_Counts",
        "Subjects",
        "p",
        "OR",
        "OR_95._CI_l",
        "OR_95._CI_u",
        "CHROMOSOME",
        "LOCATION",
        "controls",
        "cases",
        "eaf.controls"
      ],
      "rows": 98,
      "table": true,
      "tojson": true
    },
    {
      "name": "refdat_1000G_superpops",
      "title": "A dataset of reference allele frequencies from 1000 genomes superpopulations",
      "object": "refdat_1000G_superpops",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CHR",
        "SNP",
        "minor_allele",
        "major_allele",
        "MAF",
        "NCHROBS",
        "population"
      ],
      "rows": 13782,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ara_test_dat",
      "title": "A example dataset of genetic summary data for arachidonic acid",
      "topics": [
        "ara_test_dat"
      ]
    },
    {
      "page": "charge_top_hits",
      "title": "GWAS top hits for arachidonic acid in the CHARGE consortium",
      "topics": [
        "charge_top_hits"
      ]
    },
    {
      "page": "charge_top_hits_cleaned",
      "title": "GWAS top hits for arachidonic acid in the CHARGE consortium after post-GWAS cleaning",
      "topics": [
        "charge_top_hits_cleaned"
      ]
    },
    {
      "page": "combine_plots",
      "title": "Make cow plot",
      "topics": [
        "combine_plots"
      ]
    },
    {
      "page": "compare_effect_to_gwascatalog",
      "title": "Compare the genetic effect sizes in the test dataset to the GWAS catalog",
      "topics": [
        "compare_effect_to_gwascatalog"
      ]
    },
    {
      "page": "compare_effect_to_gwascatalog2",
      "title": "Compare the genetic effect sizes in the test dataset to the GWAS catalog",
      "topics": [
        "compare_effect_to_gwascatalog2"
      ]
    },
    {
      "page": "extract_sig_snps",
      "title": "Extract SNPs with P value below a specified threshold (e.g. significant SNPs)",
      "topics": [
        "extract_sig_snps"
      ]
    },
    {
      "page": "extract_snps",
      "title": "Extract SNPs",
      "topics": [
        "extract_snps"
      ]
    },
    {
      "page": "find_hits_in_gwas_catalog",
      "title": "Are hits in the GWAS catalog?",
      "topics": [
        "find_hits_in_gwas_catalog"
      ]
    },
    {
      "page": "flag_af_conflicts",
      "title": "Flag allele frequency conflicts",
      "topics": [
        "flag_af_conflicts"
      ]
    },
    {
      "page": "flag_gc_conflicts",
      "title": "Flag conflicts with the GWAS catalog",
      "topics": [
        "flag_gc_conflicts"
      ]
    },
    {
      "page": "flag_gc_conflicts2",
      "title": "Flag conflicts with the GWAS catalog",
      "topics": [
        "flag_gc_conflicts2"
      ]
    },
    {
      "page": "format_data",
      "title": "format data",
      "topics": [
        "format_data"
      ]
    },
    {
      "page": "get_efo",
      "title": "get efo",
      "topics": [
        "get_efo"
      ]
    },
    {
      "page": "glioma_test_dat",
      "title": "A example dataset of genetic summary data",
      "topics": [
        "glioma_test_dat"
      ]
    },
    {
      "page": "gwas_catalog_hits",
      "title": "GWAS top hits",
      "topics": [
        "gwas_catalog_hits"
      ]
    },
    {
      "page": "infer_ancestry",
      "title": "Infer ancestry",
      "topics": [
        "infer_ancestry"
      ]
    },
    {
      "page": "make_plot_gwas_catalog",
      "title": "Plot comparing the test study to the GWAS catalog",
      "topics": [
        "make_plot_gwas_catalog"
      ]
    },
    {
      "page": "make_plot_maf",
      "title": "MAF plot",
      "topics": [
        "make_plot_maf"
      ]
    },
    {
      "page": "make_plot_pred_effect",
      "title": "Predicted versus reported effect sizes",
      "topics": [
        "make_plot_pred_effect"
      ]
    },
    {
      "page": "make_snplist",
      "title": "make a SNP list",
      "topics": [
        "make_snplist"
      ]
    },
    {
      "page": "predict_beta_sd",
      "title": "Predicted standardised beta",
      "topics": [
        "predict_beta_sd"
      ]
    },
    {
      "page": "predict_lnor_sh",
      "title": "Predicted log odds ratio",
      "topics": [
        "predict_lnor_sh"
      ]
    },
    {
      "page": "refdat_1000G_superpops",
      "title": "A dataset of reference allele frequencies from 1000 genomes superpopulations",
      "topics": [
        "refdat_1000G_superpops"
      ]
    },
    {
      "page": "transform_betas",
      "title": "Transform betas",
      "topics": [
        "transform_betas"
      ]
    },
    {
      "page": "zz_plot",
      "title": "ZZ plot",
      "topics": [
        "zz_plot"
      ]
    }
  ],
  "_readme": "https://github.com/MRCIEU/CheckSumStats/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "assertthat",
    "backports",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "boot",
    "brio",
    "broom",
    "cachem",
    "callr",
    "car",
    "carData",
    "cli",
    "colorspace",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "Deriv",
    "desc",
    "diffobj",
    "doBy",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "forecast",
    "Formula",
    "fracdiff",
    "fs",
    "generics",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "gridExtra",
    "gtable",
    "gwasrapidd",
    "highr",
    "hms",
    "httr",
    "httr2",
    "ieugwasr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "modelr",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "pbkrtest",
    "pillar",
    "pingr",
    "pkgbuild",
    "pkgconfig",
    "pkgload",
    "plyr",
    "png",
    "polynom",
    "praise",
    "prettyunits",
    "processx",
    "progress",
    "ps",
    "purrr",
    "quantreg",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "rprojroot",
    "RSQLite",
    "rstatix",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "testthat",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "timeDate",
    "triebeard",
    "urca",
    "urltools",
    "utf8",
    "vctrs",
    "viridisLite",
    "waldo",
    "withr",
    "writexl",
    "xfun",
    "xml2",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_score": 3.113943352306837,
  "_indexed": true,
  "_nocasepkg": "checksumstats",
  "_universes": [
    "mrcieu",
    "mightyphil2000"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.0.9000",
      "date": "2026-05-19T08:09:58.000Z",
      "distro": "noble",
      "commit": "ba670767d42a9f6041b65e4a155b64a3ac096434",
      "fileid": "d276611f45079e82f620434995d523a18b13da7303327190df8b6224096d1dc6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26084386107"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.0.0.9000",
      "date": "2026-05-19T08:10:08.000Z",
      "distro": "noble",
      "commit": "ba670767d42a9f6041b65e4a155b64a3ac096434",
      "fileid": "3bb9aef571f4c12b7eebce11bd498b19d1f4bf496c6eb16b87d2516fca2bc147",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26084386107"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.0.9000",
      "date": "2026-05-19T08:09:05.000Z",
      "commit": "ba670767d42a9f6041b65e4a155b64a3ac096434",
      "fileid": "d869ee69831b2b8e36c5918f9eeef6b2339104114888c70660815280eff66936",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26084386107"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.0.0.9000",
      "date": "2026-05-19T08:09:21.000Z",
      "commit": "ba670767d42a9f6041b65e4a155b64a3ac096434",
      "fileid": "f40e9e6f901af89191d4958596ed4e6f356b88b1db10fbaf2d57b5db8721b695",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26084386107"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-05-19T08:08:47.000Z",
      "commit": "ba670767d42a9f6041b65e4a155b64a3ac096434",
      "fileid": "3b7689642cb6bd4390ed3e91d8f89b15f8005cc174c3f32307451565d21595f0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26084386107"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-05-19T08:08:52.000Z",
      "commit": "ba670767d42a9f6041b65e4a155b64a3ac096434",
      "fileid": "732258030206a1ba2d4854f31ea894f9b0e30be59fb42ed5fa185aecd62ff4a6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26084386107"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-05-19T08:08:46.000Z",
      "commit": "ba670767d42a9f6041b65e4a155b64a3ac096434",
      "fileid": "92be05c9ca74e4331b7e05b4e32a5a0fa5b7fdbaa1ef2e69e0a4d797dda1c940",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26084386107"
    }
  ]
}