{
  "_id": "6a2a59bd7b7a29ca6003ab36",
  "Package": "leo.gwas",
  "Title": "Layered Exploratory Omics (LEO)",
  "Version": "0.0.2",
  "Authors@R": "person(\"Ao\", \"Lu\", , \"luao@stu.cqmu.edu.cn\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0009-0001-0927-4468\"))",
  "Description": "Although in early development, the Layered Exploratory\nOmics (LEO) is a tool specifically designed for deep analysis\nof genomic data. It employs a multi-layered exploratory\napproach to help researchers uncover the complex biological\ninformation hidden behind their data.",
  "URL": "https://laleoarrow.github.io/leo.gwas/",
  "License": "file LICENSE",
  "Remotes": [
    "github::MRCIEU/ieugwasr",
    "github::MRCIEU/TwoSampleMR",
    "github::catboost/catboost/catboost/R-package",
    "github::laleoarrow/leo.basic",
    "github::stephenturner/annotables",
    "github::n-mounier/MRlap"
  ],
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev make libharfbuzz-dev libbz2-dev\nlibicu-dev libjpeg-dev liblzma-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev",
  "Repository": "https://laleoarrow.r-universe.dev",
  "Date/Publication": "2026-03-15 09:04:55 UTC",
  "RemoteUrl": "https://github.com/laleoarrow/leo.gwas",
  "RemoteRef": "HEAD",
  "RemoteSha": "2d18ab01483460a980bafe5f015ede4a500bdd66",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-10 12:09:33 UTC",
    "User": "root"
  },
  "Author": "Ao Lu [aut, cre, cph] (ORCID: <https://orcid.org/0009-0001-0927-4468>)",
  "Maintainer": "Ao Lu <luao@stu.cqmu.edu.cn>",
  "MD5sum": "fd846016143d569468a1d4d574f87adf",
  "_user": "laleoarrow",
  "_type": "src",
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  "_created": "2026-06-10T12:09:33.000Z",
  "_published": "2026-06-11T06:46:21.207Z",
  "_distro": "noble",
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  "_buildurl": "https://github.com/r-universe/laleoarrow/actions/runs/27274778241",
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  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/laleoarrow/leo.gwas",
  "_commit": {
    "id": "2d18ab01483460a980bafe5f015ede4a500bdd66",
    "author": "Ao Lu <luao@stu.cqmu.edu.cn>",
    "committer": "Ao Lu <luao@stu.cqmu.edu.cn>",
    "message": "20260315: finalized csMR tools but it turns out that csMR is really suck and unstable so I personally would not use it (it suck for a reason\n",
    "time": 1773565495
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      "name": "v0.0.2",
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  "_topics": [
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  "_stars": 3,
  "_contributors": [
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  "_assets": [
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  "_exports": [
    "across_df_na",
    "across_df_TF",
    "add_chrpos",
    "add_rsid",
    "add_rsid_using_ref",
    "annotate_cpg_sites",
    "any_na",
    "catboost_prs",
    "catboost_prs_rank",
    "catboost_prs_target",
    "check_significant_SNP",
    "chisq_p_value",
    "clump_data_local",
    "combine_rank",
    "combine_smr_res_1outcome",
    "combine_smr_res_chr",
    "correlation_calculate",
    "correlation_draw",
    "count_duplicate_element",
    "count_matching_elements",
    "csMR_env",
    "csMR_step1_prep",
    "csMR_step2_config.yml",
    "csMR_step3_run",
    "dr.prs",
    "extract_instruments_local",
    "fetch_same_direcrtion",
    "filter_chr_basedonSNP_p",
    "filter_chr_basedonSNP_p_qtltools",
    "get_biallelic_snp",
    "get_id",
    "group_comparison_draw",
    "HLA_exclude",
    "HLA_get",
    "lasso_prs",
    "lasso_prs_rank",
    "lasso_prs_target",
    "ld_ps_index",
    "leo_iterator",
    "leo_map_GtoCP",
    "leo_smr_adjust",
    "leo_smr_adjust_loop",
    "leo_smr_extract_sig_res",
    "leo_smr_merge_shared_probes",
    "locuszoomr_loc",
    "map_ensg_to_chrbp_using_biomaRt",
    "map_ensg_to_gene_using_biomaRt",
    "map_ensg_to_gene_using_org.Hs.eg.db",
    "map_ensg_to_tss_using_biomaRt",
    "map_gene_class_using_annotables",
    "map_gene_class_using_biomarRt",
    "map_gene_to_chrbp_using_biomaRt",
    "map_gene_to_chrbp_using_gtf",
    "map_gene_to_chrbp_using_TxDb",
    "map_gene_to_ensembl",
    "map_gene_to_tss_using_gtf",
    "mr_one_pair",
    "mr_scatter_plot_modified",
    "mrlap_one_pair",
    "plink_clump_hla_aware",
    "plot_gsMap",
    "plot_gsMap_color",
    "save_regional_plot"
  ],
  "_help": [
    {
      "page": "across_df_na",
      "title": "Across a df to count na",
      "topics": [
        "across_df_na"
      ]
    },
    {
      "page": "across_df_TF",
      "title": "Across a df to count TRUE and FALSE",
      "topics": [
        "across_df_TF"
      ]
    },
    {
      "page": "add_chrpos",
      "title": "Convert rsID to CHR & BP",
      "topics": [
        "add_chrpos"
      ]
    },
    {
      "page": "add_rsid",
      "title": "Convert CHR:BP to rsID (not recommended)",
      "topics": [
        "add_rsid"
      ]
    },
    {
      "page": "add_rsid_using_ref",
      "title": "Add rsID based on local reference file (recommended)",
      "topics": [
        "add_rsid_using_ref"
      ]
    },
    {
      "page": "annotate_cpg_sites",
      "title": "Annotate CpG Sites with Gene Information",
      "topics": [
        "annotate_cpg_sites"
      ]
    },
    {
      "page": "catboost_prs",
      "title": "CatBoost PRS utilities",
      "topics": [
        "catboost_prs",
        "catboost_prs_rank",
        "catboost_prs_target"
      ]
    },
    {
      "page": "check_significant_SNP",
      "title": "locate the significant SNP for conditional analysis",
      "topics": [
        "check_significant_SNP"
      ]
    },
    {
      "page": "chisq_p_value",
      "title": "Give precise p-value for chi-square test",
      "topics": [
        "chisq_p_value"
      ]
    },
    {
      "page": "clump_data_local",
      "title": "Perform LD Clumping Locally or via Reference Panel",
      "topics": [
        "clump_data_local"
      ]
    },
    {
      "page": "combine_smr_res_1outcome",
      "title": "Combine '.fdr' files for one or multiple outcomes (seperately)",
      "topics": [
        "combine_smr_res_1outcome"
      ]
    },
    {
      "page": "combine_smr_res_chr",
      "title": "Combine SMR Results for All Chromosomes",
      "topics": [
        "combine_smr_res_chr"
      ]
    },
    {
      "page": "correlation_calculate",
      "title": "Calculate Correlation between Two Vectors",
      "topics": [
        "correlation_calculate"
      ]
    },
    {
      "page": "correlation_draw",
      "title": "Draw Correlation between Two Vectors",
      "topics": [
        "correlation_draw"
      ]
    },
    {
      "page": "count_duplicate_element",
      "title": "Count or Identify Duplicates in a Vector",
      "topics": [
        "count_duplicate_element"
      ]
    },
    {
      "page": "count_matching_elements",
      "title": "Count or Identify Matches of a Pattern in a Vector",
      "topics": [
        "count_matching_elements"
      ]
    },
    {
      "page": "csMR_env",
      "title": "Configure Conda Environment for csMR",
      "topics": [
        "csMR_env"
      ]
    },
    {
      "page": "csMR_step1_prep",
      "title": "Prepare csMR Step1 Input",
      "topics": [
        "csMR_step1_prep"
      ]
    },
    {
      "page": "csMR_step2_config.yml",
      "title": "Build csMR config.yml",
      "topics": [
        "csMR_step2_config.yml"
      ]
    },
    {
      "page": "csMR_step3_run",
      "title": "Run csMR Step 3",
      "topics": [
        "csMR_step3_run"
      ]
    },
    {
      "page": "dr.prs",
      "title": "DuoRank PRS (Dr.PRS)",
      "topics": [
        "combine_rank",
        "dr.prs"
      ]
    },
    {
      "page": "extract_instruments_local",
      "title": "Extract instruments locally for MR Analysis",
      "topics": [
        "extract_instruments_local"
      ]
    },
    {
      "page": "filter_chr_basedonSNP_p",
      "title": "Filter Chromosomes Based on SNP P-value Threshold",
      "topics": [
        "filter_chr_basedonSNP_p"
      ]
    },
    {
      "page": "filter_chr_basedonSNP_p_qtltools",
      "title": "Filter Chromosomes Based on SNP P-value Threshold for '.qtltoolsnomi' files",
      "topics": [
        "filter_chr_basedonSNP_p_qtltools"
      ]
    },
    {
      "page": "find_proxy",
      "title": "find_proxy",
      "topics": [
        "find_proxy"
      ]
    },
    {
      "page": "format_outcome",
      "title": "format outcome data",
      "topics": [
        "format_outcome"
      ]
    },
    {
      "page": "get_id",
      "title": "Get Unique Identifier for Genetic Data",
      "topics": [
        "get_id"
      ]
    },
    {
      "page": "group_comparison_draw",
      "title": "Draw Group Comparison for a Continuous Variable",
      "topics": [
        "group_comparison_draw"
      ]
    },
    {
      "page": "HLA_exclude",
      "title": "Exclude HLA region from genomic summary data",
      "topics": [
        "HLA_exclude"
      ]
    },
    {
      "page": "HLA_get",
      "title": "Extract HLA region from genomic summary data",
      "topics": [
        "HLA_get"
      ]
    },
    {
      "page": "lasso_prs",
      "title": "Iterative Lasso PRS (iLasso) utilities",
      "topics": [
        "lasso_prs",
        "lasso_prs_rank",
        "lasso_prs_target"
      ]
    },
    {
      "page": "ld_ps_index",
      "title": "Loci_plot: Calculate the LD-matrix (LD r2) for the index SNP",
      "topics": [
        "ld_ps_index"
      ]
    },
    {
      "page": "leo_iterator",
      "title": "Leo batch iterator builder",
      "topics": [
        "leo_iterator"
      ]
    },
    {
      "page": "leo_map_GtoCP",
      "title": "Map Gene Symbols to Genomic Positions",
      "topics": [
        "leo_map_GtoCP"
      ]
    },
    {
      "page": "leo_scale_color",
      "title": "Apply Color Palette to ggplot",
      "topics": [
        "leo_scale_color"
      ]
    },
    {
      "page": "leo_smr_adjust",
      "title": "Adjust SMR Results with FDR and Bonferroni Corrections",
      "topics": [
        "leo_smr_adjust"
      ]
    },
    {
      "page": "leo_smr_adjust_loop",
      "title": "Batch Adjust SMR Results with FDR and Bonferroni Corrections",
      "topics": [
        "leo_smr_adjust_loop"
      ]
    },
    {
      "page": "leo_smr_extract_sig_res",
      "title": "Extract significant results from '.all' files",
      "topics": [
        "leo_smr_extract_sig_res"
      ]
    },
    {
      "page": "leo_smr_merge_shared_probes",
      "title": "Merge multiple SMR files and keep only shared probes for 2 outcomes",
      "topics": [
        "leo_smr_merge_shared_probes"
      ]
    },
    {
      "page": "leo.gwas_qc",
      "title": "GWAS summary QC pipeline (chip + imputed)",
      "topics": [
        "leo.gwas_qc"
      ]
    },
    {
      "page": "locuszoomr_loc",
      "title": "Loci_plot: prepare the locus data for locuszoomr",
      "topics": [
        "locuszoomr_loc"
      ]
    },
    {
      "page": "map_ensg_to_chrbp_using_biomaRt",
      "title": "Map Ensembl Gene IDs to Genomic Positions using biomaRt",
      "topics": [
        "map_ensg_to_chrbp_using_biomaRt"
      ]
    },
    {
      "page": "map_ensg_to_gene_using_biomaRt",
      "title": "Map Ensembl Gene IDs to Gene Symbols using biomaRt",
      "topics": [
        "map_ensg_to_gene_using_biomaRt"
      ]
    },
    {
      "page": "map_ensg_to_gene_using_org.Hs.eg.db",
      "title": "Map Ensembl IDs to Gene Symbols using 'org.Hs.eg.db'",
      "topics": [
        "map_ensg_to_gene_using_org.Hs.eg.db"
      ]
    },
    {
      "page": "map_ensg_to_tss_using_biomaRt",
      "title": "Map Ensembl Gene IDs to TSS Using biomaRt",
      "topics": [
        "map_ensg_to_tss_using_biomaRt"
      ]
    },
    {
      "page": "map_gene_class_using_annotables",
      "title": "Map Gene Symbols to biotype & description via *annotables*",
      "topics": [
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