{
  "_id": "6a1688ffacfb0bcc41d76249",
  "Package": "plinkQC",
  "Type": "Package",
  "Title": "Genotype Quality Control with 'PLINK'",
  "Version": "1.1.0",
  "Authors@R": "c(\nperson(\"Hannah\", \"Meyer\", email = \"hannah.v.meyer@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4564-0899\")),\nperson(\"Caroline\", \"Walter\", email= \"carowalter26@hotmail.com\",\nrole = c(\"ctb\")),\nperson(\"Maha\", \"Syed\", email= \"maha.s.syed@gmail.com\",\nrole = c(\"ctb\")))",
  "URL": "https://meyer-lab-cshl.github.io/plinkQC/",
  "BugReports": "https://github.com/meyer-lab-cshl/plinkQC/issues",
  "Maintainer": "Hannah Meyer <hannah.v.meyer@gmail.com>",
  "Description": "Genotyping arrays enable the direct measurement of an\nindividuals genotype at thousands of markers. 'plinkQC'\nfacilitates genotype quality control for genetic association\nstudies as described by Anderson and colleagues (2010)\n<doi:10.1038/nprot.2010.116>. It makes 'PLINK' basic statistics\n(e.g. missing genotyping rates per individual, allele\nfrequencies per genetic marker) and relationship functions\naccessible from 'R' and generates a per-individual and\nper-marker quality control report. Individuals and markers that\nfail the quality control can subsequently be removed to\ngenerate a new, clean dataset. Removal of individuals based on\nrelationship status is optimised to retain as many individuals\nas possible in the study. Additionally, there is a trained\nclassifier to predict genomic ancestry of human samples.",
  "License": "MIT + file LICENSE",
  "SystemRequirements": "plink (1.9)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev",
  "Repository": "https://meyer-lab-cshl.r-universe.dev",
  "Date/Publication": "2026-03-27 16:10:50 UTC",
  "RemoteUrl": "https://github.com/meyer-lab-cshl/plinkqc",
  "RemoteRef": "HEAD",
  "RemoteSha": "800cce05349d211e67203e89f511c72df3a760fb",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-27 05:58:49 UTC",
    "User": "root"
  },
  "Author": "Hannah Meyer [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4564-0899>),\nCaroline Walter [ctb],\nMaha Syed [ctb]",
  "MD5sum": "a4955a96e9b4a504b5e1a5a53461e71b",
  "_user": "meyer-lab-cshl",
  "_type": "src",
  "_file": "plinkQC_1.1.0.tar.gz",
  "_fileid": "5de9a3e82b555758a8767fb3d8184e81a60a47f9938bae8d24287c41f917ef2f",
  "_filesize": 6333990,
  "_sha256": "5de9a3e82b555758a8767fb3d8184e81a60a47f9938bae8d24287c41f917ef2f",
  "_created": "2026-05-27T05:58:49.000Z",
  "_published": "2026-05-27T06:02:39.404Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78016873404,
      "time": 172,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7233036327"
    },
    {
      "job": 78016873382,
      "time": 161,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233033750"
    },
    {
      "job": 78016873458,
      "time": 143,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7233024774"
    },
    {
      "job": 78016873378,
      "time": 188,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233031438"
    },
    {
      "job": 78016462602,
      "time": 230,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7232997583"
    },
    {
      "job": 78016873381,
      "time": 134,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233027168"
    },
    {
      "job": 78016873379,
      "time": 127,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7233025608"
    },
    {
      "job": 78016873384,
      "time": 107,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7233021088"
    },
    {
      "job": 78016873395,
      "time": 108,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233021364"
    }
  ],
  "_buildurl": "https://github.com/r-universe/meyer-lab-cshl/actions/runs/26435906994",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/meyer-lab-cshl/plinkqc",
  "_commit": {
    "id": "800cce05349d211e67203e89f511c72df3a760fb",
    "author": "Maha Syed <syed@cshl.edu>",
    "committer": "Maha Syed <syed@cshl.edu>",
    "message": "Updates to index and news portion of website\n",
    "time": 1774627850
  },
  "_maintainer": {
    "name": "Hannah Meyer",
    "email": "hannah.v.meyer@gmail.com",
    "orcid": "0000-0003-4564-0899"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "optparse",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.11.0",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "UpSetR",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "version": ">= 1.2.4",
      "role": "Imports"
    },
    {
      "package": "sys",
      "role": "Imports"
    },
    {
      "package": "randomForest",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "mockery",
      "role": "Suggests"
    },
    {
      "package": "formatR",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "meyer-lab-cshl",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-47",
      "n": 11
    },
    {
      "week": "2025-48",
      "n": 11
    },
    {
      "week": "2026-06",
      "n": 1
    },
    {
      "week": "2026-07",
      "n": 1
    },
    {
      "week": "2026-13",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 67,
  "_contributors": [
    {
      "user": "hannahvmeyer",
      "count": 358,
      "uuid": 5570947
    },
    {
      "user": "maha-syed",
      "count": 67,
      "uuid": 125997454
    },
    {
      "user": "eg-r",
      "count": 1,
      "uuid": 12281198
    }
  ],
  "_userbio": {
    "uuid": 49004558,
    "type": "organization",
    "name": "Meyer Laboratory"
  },
  "_downloads": {
    "count": 664,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/plinkQC"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/meyer-lab-cshl/plinkqc",
  "_pkgdown": "https://meyer-lab-cshl.github.io/plinkQC/",
  "_searchresults": 58,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/plinkQC.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/meyer-lab-cshl/plinkqc",
  "_realowner": "meyer-lab-cshl",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2018-11-04"
    },
    {
      "version": "0.1.1",
      "date": "2018-11-06"
    },
    {
      "version": "0.2.0",
      "date": "2018-11-09"
    },
    {
      "version": "0.2.1",
      "date": "2019-03-04"
    },
    {
      "version": "0.2.2",
      "date": "2019-06-19"
    },
    {
      "version": "0.2.3",
      "date": "2019-09-25"
    },
    {
      "version": "0.3.0",
      "date": "2019-10-19"
    },
    {
      "version": "0.3.2",
      "date": "2020-07-07"
    },
    {
      "version": "0.3.3",
      "date": "2021-02-08"
    },
    {
      "version": "0.3.4",
      "date": "2021-07-15"
    },
    {
      "version": "1.0.0",
      "date": "2025-11-25"
    },
    {
      "version": "1.0.1",
      "date": "2026-02-16"
    },
    {
      "version": "1.1.0",
      "date": "2026-03-27"
    }
  ],
  "_exports": [
    "ancestry_prediction",
    "check_het_and_miss",
    "check_hwe",
    "check_maf",
    "check_relatedness",
    "check_sex",
    "check_snp_missingness",
    "checkFiltering",
    "checkLoadingMat",
    "checkPlink",
    "checkPlink2",
    "checkRF_path",
    "cleanData",
    "convert_from_vcf",
    "convert_to_plink2",
    "evaluate_ancestry_prediction",
    "evaluate_check_het_and_miss",
    "evaluate_check_relatedness",
    "evaluate_check_sex",
    "overviewPerIndividualQC",
    "overviewPerMarkerQC",
    "perIndividualQC",
    "perMarkerQC",
    "pruning_ld",
    "relatednessFilter",
    "rename_variant_identifiers",
    "run_ancestry_format",
    "run_ancestry_prediction",
    "run_check_heterozygosity",
    "run_check_missingness",
    "run_check_relatedness",
    "run_check_sex",
    "testNumerics"
  ],
  "_help": [
    {
      "page": "ancestry_prediction",
      "title": "Predicting sample superpopulation ancestry",
      "topics": [
        "ancestry_prediction"
      ]
    },
    {
      "page": "check_het_and_miss",
      "title": "Identification of individuals with outlying missing genotype or heterozygosity rates",
      "topics": [
        "check_het_and_miss"
      ]
    },
    {
      "page": "check_hwe",
      "title": "Identification of SNPs showing a significant deviation from Hardy-Weinberg- equilibrium (HWE)",
      "topics": [
        "check_hwe"
      ]
    },
    {
      "page": "check_maf",
      "title": "Identification of SNPs with low minor allele frequency",
      "topics": [
        "check_maf"
      ]
    },
    {
      "page": "check_relatedness",
      "title": "Identification of related individuals",
      "topics": [
        "check_relatedness"
      ]
    },
    {
      "page": "check_sex",
      "title": "Identification of individuals with discordant sex information",
      "topics": [
        "check_sex"
      ]
    },
    {
      "page": "check_snp_missingness",
      "title": "Identification of SNPs with high missingness rate",
      "topics": [
        "check_snp_missingness"
      ]
    },
    {
      "page": "checkFiltering",
      "title": "Check and construct PLINK sample and marker filters",
      "topics": [
        "checkFiltering"
      ]
    },
    {
      "page": "checkLoadingMat",
      "title": "Checking the path of the loading matrix",
      "topics": [
        "checkLoadingMat"
      ]
    },
    {
      "page": "checkPlink",
      "title": "Check PLINK software access",
      "topics": [
        "checkPlink"
      ]
    },
    {
      "page": "checkPlink2",
      "title": "Check PLINK2 software access",
      "topics": [
        "checkPlink2"
      ]
    },
    {
      "page": "checkRemoveIDs",
      "title": "Check and construct individual IDs to be removed",
      "topics": [
        "checkRemoveIDs"
      ]
    },
    {
      "page": "checkRF_path",
      "title": "Checking the path of userinputted random forest",
      "topics": [
        "checkRF_path"
      ]
    },
    {
      "page": "cleanData",
      "title": "Create plink dataset with individuals and markers passing quality control",
      "topics": [
        "cleanData"
      ]
    },
    {
      "page": "convert_from_vcf",
      "title": "Converting VCF data files into PLINK v1.9 and PLINK v2.0 data files",
      "topics": [
        "convert_from_vcf"
      ]
    },
    {
      "page": "convert_to_plink2",
      "title": "Converting PLINK v1.9 data files into PLINK v2.0 data files",
      "topics": [
        "convert_to_plink2"
      ]
    },
    {
      "page": "evaluate_ancestry_prediction",
      "title": "Predicting sample superpopulation ancestry",
      "topics": [
        "evaluate_ancestry_prediction"
      ]
    },
    {
      "page": "evaluate_check_het_and_miss",
      "title": "Evaluate results from PLINK missing genotype and heterozygosity rate check.",
      "topics": [
        "evaluate_check_het_and_miss"
      ]
    },
    {
      "page": "evaluate_check_relatedness",
      "title": "Evaluate results from PLINK IBD estimation.",
      "topics": [
        "evaluate_check_relatedness"
      ]
    },
    {
      "page": "evaluate_check_sex",
      "title": "Evaluate results from PLINK sex check.",
      "topics": [
        "evaluate_check_sex"
      ]
    },
    {
      "page": "overviewPerIndividualQC",
      "title": "Overview of per sample QC",
      "topics": [
        "overviewPerIndividualQC"
      ]
    },
    {
      "page": "overviewPerMarkerQC",
      "title": "Overview of per marker QC",
      "topics": [
        "overviewPerMarkerQC"
      ]
    },
    {
      "page": "perIndividualQC",
      "title": "Quality control for all individuals in plink-dataset",
      "topics": [
        "perIndividualQC"
      ]
    },
    {
      "page": "perMarkerQC",
      "title": "Quality control for all markers in plink-dataset",
      "topics": [
        "perMarkerQC"
      ]
    },
    {
      "page": "pruning_ld",
      "title": "Pruning of SNPs in Linkage Disequilibrium",
      "topics": [
        "pruning_ld"
      ]
    },
    {
      "page": "relatednessFilter",
      "title": "Remove related individuals while keeping maximum number of individuals",
      "topics": [
        "relatednessFilter"
      ]
    },
    {
      "page": "rename_variant_identifiers",
      "title": "Renaming variants",
      "topics": [
        "rename_variant_identifiers"
      ]
    },
    {
      "page": "run_ancestry_format",
      "title": "Running functions to format data for ancestry prediction",
      "topics": [
        "run_ancestry_format"
      ]
    },
    {
      "page": "run_ancestry_prediction",
      "title": "Projecting the study data set onto the PC space of the reference dataset",
      "topics": [
        "run_ancestry_prediction"
      ]
    },
    {
      "page": "run_check_heterozygosity",
      "title": "Run PLINK heterozygosity rate calculation",
      "topics": [
        "run_check_heterozygosity"
      ]
    },
    {
      "page": "run_check_missingness",
      "title": "Run PLINK missingness rate calculation",
      "topics": [
        "run_check_missingness"
      ]
    },
    {
      "page": "run_check_relatedness",
      "title": "Run PLINK IBD estimation",
      "topics": [
        "run_check_relatedness"
      ]
    },
    {
      "page": "run_check_sex",
      "title": "Run PLINK sexcheck",
      "topics": [
        "run_check_sex"
      ]
    },
    {
      "page": "testNumerics",
      "title": "Test lists for different properties of numerics",
      "topics": [
        "testNumerics"
      ]
    }
  ],
  "_readme": "https://github.com/meyer-lab-cshl/plinkqc/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cowplot",
    "cpp11",
    "data.table",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "ggrepel",
    "glue",
    "gridExtra",
    "gtable",
    "igraph",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "optparse",
    "pillar",
    "pkgconfig",
    "plyr",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "randomForest",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "UpSetR",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "Genomes1000.Rmd",
      "filename": "Genomes1000.html",
      "title": "Processing 1000 Genomes reference data for ancestry estimation",
      "author": "Hannah Meyer",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Workflow",
        "Set-up",
        "PLINK software",
        "Download and decompress 1000 Genomes phase 3 data",
        "Convert 1000 Genomes phase 3 data to plink 1 binary format",
        "References"
      ],
      "created": "2018-10-31 18:07:22",
      "modified": "2026-02-10 15:08:10",
      "commits": 14
    },
    {
      "source": "AncestryCheck.Rmd",
      "filename": "AncestryCheck.html",
      "title": "Training a Random Forest Classifier for Population Structure Identification",
      "author": "Maha Syed and Caroline Walter",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Download reference data",
        "Set-up",
        "Match study genotypes and reference data",
        "Filter reference and study data for non A-T or G-C SNPs",
        "Renaming variant identifiers",
        "Filtering out shared SNPs between study and reference dataset",
        "Conducting markerQC, pruning LD, and individual QC",
        "PCA",
        "Training a random forest classifier in R",
        "Predicting ancestries of new study data",
        "Evalulating and Tuning of Classification Model",
        "Parameter Tuning via Grid Search",
        "Evaluating/Interpretting the RF",
        "References"
      ],
      "created": "2018-10-23 15:46:34",
      "modified": "2026-03-27 16:09:55",
      "commits": 36
    },
    {
      "source": "plinkQC.Rmd",
      "filename": "plinkQC.html",
      "title": "Genotype quality control with plinkQC",
      "author": "Hannah Meyer and Maha Syed",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Per-individual quality control",
        "Per-marker quality control",
        "Clean data",
        "Workflow",
        "Create QC-ed dataset",
        "Step-by-step",
        "Individuals with discordant sex information",
        "Individuals with outlying missing genotype and/or heterozygosity rates",
        "Related individualis",
        "Ancestry Predictions of Data",
        "Markers with excessive missingness rate",
        "Markers with deviation from HWE",
        "Markers with low minor allele frequency",
        "References"
      ],
      "created": "2018-10-20 17:27:11",
      "modified": "2026-03-27 16:09:55",
      "commits": 24
    },
    {
      "source": "HapMap.Rmd",
      "filename": "HapMap.html",
      "title": "Processing HapMap III reference data for ancestry estimation",
      "author": "Hannah Meyer",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Workflow",
        "Set-up",
        "Download and convert Hapmap phase III data",
        "Update annotation",
        "Update the reference data",
        "References"
      ],
      "created": "2018-10-24 14:52:26",
      "modified": "2026-02-10 15:08:10",
      "commits": 8
    },
    {
      "source": "my-vignette.Rmd",
      "filename": "my-vignette.html",
      "title": "my-vignette",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2025-11-17 17:29:32",
      "modified": "2025-11-17 17:29:32",
      "commits": 1
    }
  ],
  "_score": 7.987442804935801,
  "_indexed": true,
  "_nocasepkg": "plinkqc",
  "_universes": [
    "meyer-lab-cshl"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-27T06:01:21.000Z",
      "distro": "noble",
      "commit": "800cce05349d211e67203e89f511c72df3a760fb",
      "fileid": "e6856cabe3080db2d471663f1a640adfc0b0862bf9e32b6c7a9b542d695e3ec9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/meyer-lab-cshl/actions/runs/26435906994"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-27T06:01:14.000Z",
      "distro": "noble",
      "commit": "800cce05349d211e67203e89f511c72df3a760fb",
      "fileid": "3ec77f6e01e1fdf02eacb1170dc6b81aea393fb958ec504c715fc33075680b96",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/meyer-lab-cshl/actions/runs/26435906994"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-27T06:00:53.000Z",
      "commit": "800cce05349d211e67203e89f511c72df3a760fb",
      "fileid": "99d2b796cbc74cf7856ff726fa67330e463c4472755730ef38c3aa5ccacc6269",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/meyer-lab-cshl/actions/runs/26435906994"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-27T06:01:10.000Z",
      "commit": "800cce05349d211e67203e89f511c72df3a760fb",
      "fileid": "ba5954f742fca9ea87ad94117020ddf9930932c7ff247cfe66389756032b883e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/meyer-lab-cshl/actions/runs/26435906994"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-05-27T06:01:25.000Z",
      "commit": "800cce05349d211e67203e89f511c72df3a760fb",
      "fileid": "d87b29c7dc5639f01352cb1bc986006a47a9f229da2ef1570361991e3b6e2a9c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/meyer-lab-cshl/actions/runs/26435906994"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-27T06:00:20.000Z",
      "commit": "800cce05349d211e67203e89f511c72df3a760fb",
      "fileid": "cb467cb5ec37c32ea3b85e95fc21c9a329b1e93a4a4a386a52691aaddf7770d7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/meyer-lab-cshl/actions/runs/26435906994"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-27T06:00:11.000Z",
      "commit": "800cce05349d211e67203e89f511c72df3a760fb",
      "fileid": "18e75c726dc22fde7b09124df5ecdcc353af140b6f181dcde652fe11fce7dcf7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/meyer-lab-cshl/actions/runs/26435906994"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-27T06:00:11.000Z",
      "commit": "800cce05349d211e67203e89f511c72df3a760fb",
      "fileid": "b3635e82c4dfaf8e06f892688e9a19f956403da5a866427133bdccda277ba8c7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/meyer-lab-cshl/actions/runs/26435906994"
    }
  ]
}