{
  "_id": "6ac7bdf0de46216d5edd2c88",
  "Package": "simulateGP",
  "Title": "Functions for Simulating Genotype-Phenotype Relationships",
  "Version": "0.1.3",
  "Authors@R": "c(\nperson(\"Gibran\", \"Hemani\", , \"explodecomputer@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0920-1055\")),\nperson(\"John\", \"Ferguson\", , \"john.ferguson@nuigalway.ie\", role = \"aut\"),\nperson(\"Rita\", \"Rasteiro\", , \"rita.rasteiro@bristol.ac.uk\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-4217-3060\"))\n)",
  "Description": "Functions for simulating SNP effects on phenotypes.\nFunctions for simulating disease risk on probability and\nliability scales. Simulations to quickly obtain estimates of\neffect sizes for simulated genotype-phenotypes.",
  "License": "MIT + file LICENSE",
  "URL": "https://explodecomputer.github.io/simulateGP/,\nhttps://github.com/explodecomputer/simulateGP,\nhttps://mrcieu.r-universe.dev/simulateGP",
  "BugReports": "https://github.com/explodecomputer/simulateGP/issues",
  "VignetteBuilder": "knitr",
  "Remotes": [
    "mrcieu/genetics.binaRies",
    "mrcieu/gwasglue2",
    "mrcieu/ieugwasr",
    "mrcieu/TwoSampleMR"
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  "Config/roxygen2/markdown": "TRUE",
  "Config/roxygen2/version": "8.1.0",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev",
  "Repository": "https://mrcieu.r-universe.dev",
  "Date/Publication": "2026-10-01 08:38:24 UTC",
  "RemoteUrl": "https://github.com/explodecomputer/simulateGP",
  "RemoteRef": "refs/pull/6/head",
  "RemoteSha": "dd16b78fcb43dabd3d8a83baaec39f4f4faaec9f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-08 15:55:46 UTC",
    "User": "root"
  },
  "Author": "Gibran Hemani [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0920-1055>),\nJohn Ferguson [aut],\nRita Rasteiro [aut] (ORCID: <https://orcid.org/0000-0002-4217-3060>)",
  "Maintainer": "Gibran Hemani <explodecomputer@gmail.com>",
  "_user": "mrcieu",
  "_type": "src",
  "_file": "simulateGP_0.1.3.tar.gz",
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  "_expires": "2027-01-16T15:59:42.000Z",
  "_created": "2026-10-08T15:55:46.000Z",
  "_published": "2026-10-08T15:59:44.563Z",
  "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37804060607",
  "_status": "success",
  "_host": "GitHub-Actions",
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    "email": "explodecomputer@gmail.com",
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    "description": "",
    "uuid": 1924940,
    "orcid": "0000-0003-0920-1055"
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      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dplyr",
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    },
    {
      "package": "genetics.binaRies",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "gwasglue2",
      "role": "Imports"
    },
    {
      "package": "ieugwasr",
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    {
      "package": "magrittr",
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    },
    {
      "package": "MASS",
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    },
    {
      "package": "parallel",
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    },
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    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "TwoSampleMR",
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    },
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  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "n": 6
    }
  ],
  "_tags": [],
  "_topics": [
    "genetics",
    "simulations",
    "statistics"
  ],
  "_stars": 9,
  "_contributors": [
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      "user": "explodecomputer",
      "count": 75,
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  "_pkgdown": "https://explodecomputer.github.io/simulateGP/",
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  "_rbuild": "4.6.1",
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    "extra/citation.json",
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    "extra/contents.json",
    "extra/manual.pdf",
    "extra/simulateGP.html",
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  "_cranurl": false,
  "_exports": [
    "%>%",
    "add_u",
    "allele_frequency",
    "arbitrary_map",
    "ascertain_samples",
    "choose_effects",
    "contingency",
    "correlated_binomial",
    "create_system",
    "estimate_system_effects",
    "expected_mse",
    "expected_se",
    "expected_ssx",
    "fast_assoc",
    "generate_gwas_params",
    "generate_gwas_ss",
    "generate_gwas_ss_1",
    "generate_ldobj",
    "get_effs",
    "get_ld",
    "get_population_allele_frequency",
    "get_regions_from_ldobjdir",
    "gwas",
    "gx_to_gp",
    "hap_freqs",
    "init_parameters",
    "lor_to_rsq",
    "make_geno",
    "make_mvdat",
    "make_phen",
    "merge_exp_out",
    "range01",
    "read_ldobjdir",
    "recode_dat",
    "recode_dat_intercept",
    "recode_dat_simple",
    "risk_cross_plot",
    "risk_simulation",
    "sample_beta",
    "sample_system_effects",
    "simulate_geno",
    "simulate_haplotypes",
    "simulate_population",
    "summary_set",
    "test_ldobj",
    "test_system",
    "y_to_binary"
  ],
  "_datasets": [
    {
      "name": "ldetect",
      "title": "Data frame of independent LD regions",
      "object": "ldetect",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "chr",
        "start",
        "stop",
        "pop"
      ],
      "rows": 5731,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "simulateGP-package",
      "title": "simulateGP: Functions for Simulating Genotype-Phenotype Relationships",
      "topics": [
        "simulateGP-package",
        "simulateGP",
        "simulategp"
      ]
    },
    {
      "page": "add_u",
      "title": "Add confounder variables and their instruments",
      "topics": [
        "add_u"
      ]
    },
    {
      "page": "allele_frequency",
      "title": "Estimate allele frequency from SNP",
      "topics": [
        "allele_frequency"
      ]
    },
    {
      "page": "arbitrary_map",
      "title": "Create an arbitrary map",
      "topics": [
        "arbitrary_map"
      ]
    },
    {
      "page": "ascertain_samples",
      "title": "Ascertain some proportion of cases and controls from binary phenotype",
      "topics": [
        "ascertain_samples"
      ]
    },
    {
      "page": "choose_effects",
      "title": "Get vector of effects that explain some amount of variance",
      "topics": [
        "choose_effects"
      ]
    },
    {
      "page": "contingency",
      "title": "Obtain 2x2 contingency table from marginal parameters and odds ratio",
      "topics": [
        "contingency"
      ]
    },
    {
      "page": "correlated_binomial",
      "title": "Simulate two correlated binomial variables",
      "topics": [
        "correlated_binomial"
      ]
    },
    {
      "page": "create_system",
      "title": "Wrapper for simulation pipeline",
      "topics": [
        "create_system"
      ]
    },
    {
      "page": "estimate_system_effects",
      "title": "Estimate the effects of all SNPs on all phenotypes",
      "topics": [
        "estimate_system_effects"
      ]
    },
    {
      "page": "expected_mse",
      "title": "Calculate expected MSE",
      "topics": [
        "expected_mse"
      ]
    },
    {
      "page": "expected_se",
      "title": "Expected se given beta, af, n and vy",
      "topics": [
        "expected_se"
      ]
    },
    {
      "page": "expected_ssx",
      "title": "Calculate expected SSX",
      "topics": [
        "expected_ssx"
      ]
    },
    {
      "page": "fast_assoc",
      "title": "Get summary statistics in simple linear regression",
      "topics": [
        "fast_assoc"
      ]
    },
    {
      "page": "generate_gwas_params",
      "title": "Generate SNP effects given MAF, h2 and selection",
      "topics": [
        "generate_gwas_params"
      ]
    },
    {
      "page": "generate_gwas_ss",
      "title": "Modify SNP effects to account for LD",
      "topics": [
        "generate_gwas_ss"
      ]
    },
    {
      "page": "generate_gwas_ss_1",
      "title": "Create a GWAS summary dataset",
      "topics": [
        "generate_gwas_ss_1"
      ]
    },
    {
      "page": "generate_ldobj",
      "title": "Generate LD matrix objects from reference panel",
      "topics": [
        "generate_ldobj"
      ]
    },
    {
      "page": "get_effs",
      "title": "Get effs for two traits and make dat format",
      "topics": [
        "get_effs"
      ]
    },
    {
      "page": "get_ld",
      "title": "Get LD matrix for a specified region from bfile reference panel",
      "topics": [
        "get_ld"
      ]
    },
    {
      "page": "get_population_allele_frequency",
      "title": "Estimate the allele frequency in population from case/control summary data",
      "topics": [
        "get_population_allele_frequency"
      ]
    },
    {
      "page": "get_regions_from_ldobjdir",
      "title": "Determine regions from LD file",
      "topics": [
        "get_regions_from_ldobjdir"
      ]
    },
    {
      "page": "gwas",
      "title": "Perform association of many SNPs against phenotype",
      "topics": [
        "gwas"
      ]
    },
    {
      "page": "gx_to_gp",
      "title": "Translate risk from liability to probability scale",
      "topics": [
        "gx_to_gp"
      ]
    },
    {
      "page": "hap_freqs",
      "title": "Estimate haplotype frequencies for two loci",
      "topics": [
        "hap_freqs"
      ]
    },
    {
      "page": "init_parameters",
      "title": "Choose initial parameters for direct effects on X and Y",
      "topics": [
        "init_parameters"
      ]
    },
    {
      "page": "ldetect",
      "title": "Data frame of independent LD regions",
      "topics": [
        "ldetect"
      ]
    },
    {
      "page": "lor_to_rsq",
      "title": "Estimate proportion of variance of liability explained by SNP in general population",
      "topics": [
        "lor_to_rsq"
      ]
    },
    {
      "page": "make_geno",
      "title": "Create genotype matrix",
      "topics": [
        "make_geno"
      ]
    },
    {
      "page": "make_mvdat",
      "title": "Take several exposures and one outcome and make the data required for multivariable MR",
      "topics": [
        "make_mvdat"
      ]
    },
    {
      "page": "make_phen",
      "title": "Simulate variable based on the influences of other variables",
      "topics": [
        "make_phen"
      ]
    },
    {
      "page": "merge_exp_out",
      "title": "Organise outputs from 'gwas' into harmonised dat format",
      "topics": [
        "merge_exp_out"
      ]
    },
    {
      "page": "range01",
      "title": "Scale variable to have range between 0 and 1",
      "topics": [
        "range01"
      ]
    },
    {
      "page": "read_ldobjdir",
      "title": "Read in LD objects into list",
      "topics": [
        "read_ldobjdir"
      ]
    },
    {
      "page": "recode_dat",
      "title": "Recode data to make every effect on x positive",
      "topics": [
        "recode_dat"
      ]
    },
    {
      "page": "recode_dat_intercept",
      "title": "Intercept recoding to have every effect on x positive",
      "topics": [
        "recode_dat_intercept"
      ]
    },
    {
      "page": "recode_dat_simple",
      "title": "Simple recoding to have every effect on x positive",
      "topics": [
        "recode_dat_simple"
      ]
    },
    {
      "page": "risk_cross_plot",
      "title": "Plot liability vs probability disease risk",
      "topics": [
        "risk_cross_plot"
      ]
    },
    {
      "page": "risk_simulation",
      "title": "Make simulation to compare disease and liability scales",
      "topics": [
        "risk_simulation"
      ]
    },
    {
      "page": "sample_beta",
      "title": "Sample beta values given standard errors",
      "topics": [
        "sample_beta"
      ]
    },
    {
      "page": "sample_system_effects",
      "title": "Sample the actual effects based on initial parameters",
      "topics": [
        "sample_system_effects"
      ]
    },
    {
      "page": "simulate_geno",
      "title": "Simulate genotypes from haplotypes",
      "topics": [
        "simulate_geno"
      ]
    },
    {
      "page": "simulate_haplotypes",
      "title": "Simulate haplotypes of two loci",
      "topics": [
        "simulate_haplotypes"
      ]
    },
    {
      "page": "simulate_population",
      "title": "Simulate individual level data from initial parameters",
      "topics": [
        "simulate_population"
      ]
    },
    {
      "page": "stuff",
      "title": "General funcs",
      "topics": [
        "stuff"
      ]
    },
    {
      "page": "summary_set",
      "title": "Wrapper for generating a summary set",
      "topics": [
        "summary_set"
      ]
    },
    {
      "page": "test_ldobj",
      "title": "Create test LD object",
      "topics": [
        "test_ldobj"
      ]
    },
    {
      "page": "test_system",
      "title": "Apply MR tests to system",
      "topics": [
        "test_system"
      ]
    },
    {
      "page": "y_to_binary",
      "title": "Convert continuous trait to binary",
      "topics": [
        "y_to_binary"
      ]
    }
  ],
  "_rundeps": [
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    "base64enc",
    "bslib",
    "cachem",
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  "_vignettes": [
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      "source": "gwas_summary_data.Rmd",
      "filename": "gwas_summary_data.html",
      "title": "Background notes: Simulating GWAS summary data",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Expected standard error",
        "Sampling the effect estimate",
        "Sampling a set of effect estimates",
        "Sensitivitiy to HWE"
      ],
      "created": "2020-03-03 13:11:20",
      "modified": "2021-04-06 21:01:39",
      "commits": 9
    },
    {
      "source": "susie_check.Rmd",
      "filename": "susie_check.html",
      "title": "Comparing SuSIE results with summary level vs individual level simulations",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Compare summary level simulations against individual level simulations",
        "Compare two different populations"
      ],
      "created": "2021-04-06 21:55:33",
      "modified": "2021-06-28 23:35:42",
      "commits": 2
    },
    {
      "source": "mr_dgp.rmd",
      "filename": "mr_dgp.html",
      "title": "Data generating process for genetic effects on complex traits with interactions",
      "author": "Gibran Hemani",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Genetic effects",
        "Model 1 - simple linear relationship between x and y with large numbers of instruments of small effect",
        "Model 2 - Heterogeneous treatment effect of x on y based on covariate",
        "Model 3 - The interacting variable from (2) is proxied by a large number of proxies",
        "Model 4 - Heterogeneous treatment effect at the instrument level"
      ],
      "created": "2020-04-07 22:24:06",
      "modified": "2026-09-30 13:51:31",
      "commits": 5
    },
    {
      "source": "sample_overlap_theory.Rmd",
      "filename": "sample_overlap_theory.html",
      "title": "Directly simulating summary datasets with sample overlap",
      "author": "John Ferguson",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2021-03-05 00:50:06",
      "modified": "2021-03-05 00:50:06",
      "commits": 1
    },
    {
      "source": "generate_ldobj.Rmd",
      "filename": "generate_ldobj.html",
      "title": "Generating LD matrices",
      "engine": "knitr::rmarkdown",
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