{ "_id": "6a10610bacfb0bcc41ca782c", "Package": "pleioh2g", "Type": "Package", "Title": "Estimation of Pleiotropic Heritability from Genome-Wide\nAssociation Studies (GWAS) Summary Statistics", "Version": "0.1.2", "Authors@R": "c(\nperson(given = \"Yujie\", family = \"Zhao\",\nrole = c(\"aut\", \"cre\"),\nemail = \"yujiezhao@hsph.harvard.edu\")\n)", "Description": "Provides tools to compute unbiased pleiotropic\nheritability estimates of complex diseases from genome-wide\nassociation studies (GWAS) summary statistics. We estimate\npleiotropic heritability from GWAS summary statistics by\nestimating the proportion of variance explained from an\nestimated genetic correlation matrix (Bulik-Sullivan et al.\n2015 ) and employing a Monte-Carlo bias\ncorrection procedure to account for sampling noise in genetic\ncorrelation estimates.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Language": "en-US", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-08 08:08:38 UTC", "User": "root" }, "Author": "Yujie Zhao [aut, cre]", "Maintainer": "Yujie Zhao ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-03-09 15:15:02 UTC", "RemoteUrl": "https://github.com/cran/pleioh2g", "RemoteRef": "HEAD", "RemoteSha": "91f5449772097d9843884316908faf18a0424801", "MD5sum": "9e2e198bcc6f73a428986584b1d4e468", "_user": "cran", "_type": "src", "_file": "pleioh2g_0.1.2.tar.gz", "_fileid": 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"Cal_cor_pleiotropic_h2_corrected_single" ] }, { "page": "Cal_cor_pleiotropic_h2_single", "title": "Compute single pleioh2g for target disease before correction with referred disease index in the rg matrix", "topics": [ "Cal_cor_pleiotropic_h2_single" ] }, { "page": "Cal_cor_test_single", "title": "Compute inversed elements for the target disease in bias correction procedure with referred disease index in the rg matrix", "topics": [ "Cal_cor_test_single" ] }, { "page": "Cal_rg_h2g_alltraits", "title": "Compute rg + h2g", "topics": [ "Cal_rg_h2g_alltraits" ] }, { "page": "Cal_rg_h2g_jk_alltraits", "title": "genomic-block jackknife and compute rg + h2g", "topics": [ "Cal_rg_h2g_jk_alltraits" ] }, { "page": "generate_proposal_sample_changea_cor", "title": "Generate samples based on sampling covariance matrix and rg matrix for target disease", "topics": [ "generate_proposal_sample_changea_cor" ] }, { "page": "h2_liability", "title": "Convert Heritability to Liability Scale", "topics": [ "h2_liability" ] }, { "page": "h2_vector", "title": "h2 vector for 62 traits", "topics": [ "h2_vector" ] }, { "page": "h2_vector_mat", "title": "h2 jk matrix for 62 traits", "topics": [ "h2_vector_mat" ] }, { "page": "ldsc_h2", "title": "Estimate heritability - refer to ldscr R package (https://github.com/mglev1n/ldscr)", "topics": [ "ldsc_h2" ] }, { "page": "ldsc_rg", "title": "Estimate cross-trait genetic correlations (Robust Version) - refer to ldscr R package (https://github.com/mglev1n/ldscr)", "topics": [ "ldsc_rg" ] }, { "page": "make_weights", "title": "Internal Function to make weights - refer to ldscr R package (https://github.com/mglev1n/ldscr)", "topics": [ "make_weights" ] }, { "page": "merge_sumstats", "title": "Merging summary statistics with LD-score files - refer to ldscr R package (https://github.com/mglev1n/ldscr)", "topics": [ "merge_sumstats" ] }, { "page": "perform_analysis", "title": "Internal function to perform LDSC heritability/covariance analysis - refer to ldscr R package (https://github.com/mglev1n/ldscr)", "topics": [ "perform_analysis" ] }, { "page": "pleiotropyh2_cor_computing_single", "title": "Compute pleioh2g after bias correction for target disease", "topics": [ "pleiotropyh2_cor_computing_single" ] }, { "page": "pleiotropyh2_cor_computing_single_prune", "title": "Compute pleioh2g after bias correction for target disease", "topics": [ "pleiotropyh2_cor_computing_single_prune" ] }, { "page": "pleiotropyh2_nocor_computing_single", "title": "Compute pleioh2g before bias correction for target disease", "topics": [ "pleiotropyh2_nocor_computing_single" ] }, { "page": "Prune_disease_selection_DTrgzscore", "title": "Prune disease selection", "topics": [ "Prune_disease_selection_DTrgzscore" ] }, { "page": "pruning_pleioh2g_wrapper", "title": "Perform pruning in computing pleioh2g and correct bias", "topics": [ "pruning_pleioh2g_wrapper" ] }, { "page": "read_ld", "title": "Read ld from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)", "topics": [ "read_ld" ] }, { "page": "read_m", "title": "Read M from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)", "topics": [ "read_m" ] }, { "page": "read_sumstats", "title": "Read summary statistics from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)", "topics": [ "read_sumstats" ] }, { "page": "read_wld", "title": "Read wld from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)", "topics": [ "read_wld" ] }, { "page": "Results_full_rg", "title": "Genetic correlation matrix for 62 traits", "topics": [ "Results_full_rg" ] }, { "page": "Results_full_rg_array", "title": "Jackknife array of genetic correlations (62 traits)", "topics": [ "Results_full_rg_array" ] }, { "page": "Rg_mat_z", "title": "Genetic correlation Z matrix for 62 traits", "topics": [ "Rg_mat_z" ] }, { "page": "sumstats_munged_example_input", "title": "Example munged dataframe - refer to ldscr R package (https://github.com/mglev1n/ldscr)", "topics": [ "sumstats_munged_example_input" ] } ], "_rundeps": [ "arrow", "assertthat", "backports", "bit", "bit64", "checkmate", "cli", "cpp11", "crayon", "data.table", "dplyr", "fs", "gdata", "generics", "glue", "gtools", "hms", "lifecycle", "magrittr", "mvtnorm", "pillar", "pkgconfig", "prettyunits", "progress", "purrr", "R6", "rlang", "tibble", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr" ], "_vignettes": [ { "source": "pleioh2g-tutorial.Rmd", "filename": "pleioh2g-tutorial.html", "title": "pleioh2g-tutorial", "engine": "knitr::rmarkdown", "headings": [ "Installation:", "Steps", "Step 1: Prepare LDSC input-format data for multiple traits.", "Step 2: Compute pleiotropic heritability with bias correction", "Leave-category-out analysis instruction" ], "created": "2025-10-28 09:50:02", "modified": "2025-10-28 09:50:02", "commits": 1 } ], 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