{ "_id": "6a1ed94eb401979e7340f2fd", "Package": "gwasglue2", "Title": "GWAS summary data sources connected to analytical tools", "Version": "0.0.0.9000", "Authors@R": "c(\nperson(\"Gibran\", \"Hemani\", , \"g.hemani@bristol.ac.uk\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-0920-1055\")),\nperson(\"Rita\", \"Rasteiro\", , \"rita.rasteiro@bristol.ac.uk\", role = c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0002-4217-3060\")),\nperson(\"Christopher\", \"Woods\", , \"Christopher.Woods@bristol.ac.uk\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-6563-9903\"))\n)", "Description": "Description: Many tools exist that use GWAS summary data\nfor colocalisation, fine mapping, Mendelian randomization,\nvisualisation, etc. This package is a conduit that connects R\npackages that can retrieve GWAS summary data to various tools\nfor analysing those data.", "License": "MIT + file LICENSE", "URL": "https://github.com/MRCIEU/gwasglue2", "BugReports": "https://github.com/MRCIEU/gwasglue2/issues", "VignetteBuilder": "knitr", "Remotes": [ "mrcieu/TwoSampleMR" ], "Config/testthat/edition": "3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "Collate": "'constructors.R' 'dataset.R' 'convertTo.R' 'globals.R'\n'harmonise.R' 'harmoniseLD_method.R' 'harmonise_ld.R'\n'harmonise_method.R' 'liftover.R' 'meta.R' 'plot.R'\n'summaryset.R' 'utils.R' 'wrappers.R'", "Repository": "https://mrcieu.r-universe.dev", "Date/Publication": "2023-11-28 13:12:30 UTC", "RemoteUrl": "https://github.com/MRCIEU/gwasglue2", "RemoteRef": "HEAD", "RemoteSha": "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-20 09:29:40 UTC", "User": "root" }, "Author": "Gibran Hemani [aut] (ORCID: ),\nRita Rasteiro [cre, aut] (ORCID:\n),\nChristopher Woods [aut] (ORCID:\n)", "Maintainer": "Rita Rasteiro ", "MD5sum": "2197d5a02d318071bf60c5f7407ee106", "_user": "mrcieu", "_type": "src", "_file": "gwasglue2_0.0.0.9000.tar.gz", "_fileid": "9bb0d2b10b067103310816cf32b9ed0dff02e3e825724ac624ecc89b96194a2e", "_filesize": 2253183, "_sha256": "9bb0d2b10b067103310816cf32b9ed0dff02e3e825724ac624ecc89b96194a2e", "_created": "2026-05-20T09:29:40.000Z", "_published": "2026-06-02T13:23:26.019Z", "_distro": "noble", "_jobs": [ { "job": 79080371584, "time": 180, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7106357940" }, { "job": 79080371539, "time": 185, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7106359861" }, { "job": 79080371601, "time": 117, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7106334725" }, { "job": 79080371647, "time": 107, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7106330875" }, { "job": 79080370006, "time": 235, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7106291055" }, { "job": 79080370175, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7358871055" }, { "job": 79080372064, "time": 118, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7106335592" }, { "job": 79080371641, "time": 270, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7106391139" }, { "job": 79080371275, "time": 124, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7106337228" } ], "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26153676913", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/MRCIEU/gwasglue2", "_commit": { "id": "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "author": "Rita Rasteiro ", "committer": "GitHub ", "message": "Merge pull request #59 from MRCIEU/issue-templates\n\nAdd issue templates", "time": 1701177150 }, "_maintainer": { "name": "Rita Rasteiro", "email": "rita.rasteiro@bristol.ac.uk", "login": "ritarasteiro", "orcid": "0000-0002-4217-3060", "description": "RSE @JGIBristol, University of Bristol, UK", "uuid": 5339671 }, "_registered": true, "_dependencies": [ { "package": "methods", "role": "Depends" }, { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "digest", "role": "Suggests" }, { "package": "GenomicRanges", "role": "Suggests" }, { "package": "graphics", "role": "Suggests" }, { "package": "IRanges", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "rtracklayer", "role": "Suggests" }, { "package": "stats", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "TwoSampleMR", "role": "Suggests" }, { "package": "utils", "role": "Suggests" } ], "_owner": "mrcieu", "_selfowned": true, "_usedby": 1, "_updates": [], "_tags": [], "_stars": 23, "_contributors": [ { "user": "ritarasteiro", "count": 182, "uuid": 5339671 }, { "user": "explodecomputer", "count": 26, "uuid": 1924940 } ], "_userbio": { "uuid": 15654827, "type": "organization", "name": "MRC Integrative Epidemiology Unit" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/gwasglue2" }, "_devurl": "https://github.com/mrcieu/gwasglue2", "_searchresults": 12, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gwasglue2.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "add_summaryset", "addToMetadata", "assertSameShape", "convertForTwoSampleMR", "create_dataset", "create_dataset_from_tibble", "create_metadata", "create_summary_set_from_lbf", "create_summaryset", "create_summaryset_from_gwasvcf", "create_summaryset_from_tibble", "DataSet", "dataset_to_hyprcoloc", "dimData", "download_chainfile", "getAttributes", "getData", "getLDMatrix", "getLength", "getMetadata", "getRSID", "getShape", "getSummaryData", "getSummarySet", "getTraitOrg", "getVariants", "harmonise_ld", "harmoniseData", "isHarmonised", "isHarmonisedLD", "lbf_to_z_cont", "liftover", "merge_datasets", "meta_analysis", "overlapVariants", "plot_gwasglue", "setAttributes", "setMetadata", "setRSID", "setShape", "setTraitOrg", "setVariantid", "setVariants", "setZscores", "SummarySet", "susie_to_dataset" ], "_help": [ { "page": "add_summaryset", "title": "Add a SummarySet to a DataSet", "topics": [ "add_summaryset" ] }, { "page": "addToMetadata-methods", "title": "Add to metadata in the SummarySet", "topics": [ "addToMetadata", "addToMetadata,SummarySet-method" ] }, { "page": "assertSameShape-methods", "title": "Assert if the shapes of SummarySets in the gwasglue2 DataSet are the same", "topics": [ "assertSameShape", "assertSameShape,DataSet-method" ] }, { "page": "convertForTwoSampleMR", "title": "Convert tool to TwoSampleMR format", "topics": [ "convertForTwoSampleMR", "convertForTwoSampleMR,DataSet-method" ] }, { "page": "create_dataset", "title": "Creates a DataSet object using gwasglue2 SummarySet objects, and harmonise data against data", "topics": [ "create_dataset" ] }, { "page": "create_dataset_from_tibble", "title": "Creates a DataSet object using GWAS summary statistics, and harmonise data against data", "topics": [ "create_dataset_from_tibble" ] }, { "page": "create_metadata", "title": "Metadata object", "topics": [ "create_metadata" ] }, { "page": "create_summary_set_from_lbf", "title": "Create SummarySet from log Bayes Factor", "topics": [ "create_summary_set_from_lbf" ] }, { "page": "create_summaryset", "title": "A function to create a gwasglue2 SummarySet object from different sources and formats", "topics": [ "create_summaryset" ] }, { "page": "create_summaryset_from_gwasvcf", "title": "A function to create a gwasglue2 SummarySet object from a vcf file", "topics": [ "create_summaryset_from_gwasvcf" ] }, { "page": "create_summaryset_from_tibble", "title": "A function to create a gwasglue2 SummarySet object from a tibble", "topics": [ "create_summaryset_from_tibble" ] }, { "page": "dataset_to_hyprcoloc", "title": "DataSet to hyprcoloc", "topics": [ "dataset_to_hyprcoloc" ] }, { "page": "DataSet", "title": "An S4 class to represent the Data Set", "topics": [ "DataSet", "DataSet-class" ] }, { "page": "dimData-methods", "title": "Dimensions of the GWAS Summary Statistics data", "topics": [ "dimData", "dimData,SummarySet-method" ] }, { "page": "download_chainfile", "title": "Chain files downloader", "topics": [ "download_chainfile" ] }, { "page": "getAttributes-methods", "title": "Get Method to retrieve the attributes linked to the SummarySet", "topics": [ "getAttributes", "getAttributes,SummarySet-method" ] }, { "page": "getData-methods", "title": "Get Method to retrieve the GWAS Summary Statistics", "topics": [ "getData", "getData,DataSet-method" ] }, { "page": "getLDMatrix-methods", "title": "Get Method to retrieve the Linkage Disequilibrium matrix", "topics": [ "getLDMatrix", "getLDMatrix,DataSet-method" ] }, { "page": "getLength-methods", "title": "Size of the DataSet", "topics": [ "getLength", "getLength,DataSet-method" ] }, { "page": "getMetadata-methods", "title": "Get Method to retrieve the metadata stored in the SummarySet", "topics": [ "getMetadata", "getMetadata,SummarySet-method" ] }, { "page": "getRSID-methods", "title": "Get Method to retrieve RSID/variants stored in the SummarySet", "topics": [ "getRSID", "getRSID,SummarySet-method" ] }, { "page": "getShape-methods", "title": "Get the Shape of the gwasglue2 objects", "topics": [ "getShape", "getShape,SummarySet-method" ] }, { "page": "getSummaryData-methods", "title": "Get Method to retrieve the GWAS Summary Statistics from the SummarySet", "topics": [ "getSummaryData", "getSummaryData,SummarySet-method" ] }, { "page": "getSummarySet-methods", "title": "Get Method to retrieve the gwasglue2 SummarySet object", "topics": [ "getSummarySet", "getSummarySet,DataSet-method" ] }, { "page": "getTraitOrg-methods", "title": "Get the trait organisation of the gwasglue2 DataSet", "topics": [ "getTraitOrg", "getTraitOrg,DataSet-method" ] }, { "page": "getVariants-methods", "title": "Get Method to retrieve RSID/variants stored in the SummarySet", "topics": [ "getVariants", "getVariants,SummarySet-method" ] }, { "page": "harmonise_ld", "title": "Harmonise data against LD matrix", "topics": [ "harmonise_ld" ] }, { "page": "harmonise_ld_dat", "title": "Harmonise LD matrix against summary data (now it just looks for overlaped variants. The harmonisation is done in ld_matrix_local) harmonise_ld_dat() is based TwoSampleMR::harmonise_ld_dat()", "topics": [ "harmonise_ld_dat" ] }, { "page": "harmoniseData-methods", "title": "Harmonise the alleles and effects between two summary sets", "topics": [ "harmoniseData", "harmoniseData,DataSet-method" ] }, { "page": "isHarmonised-methods", "title": "Check if the DataSet is harmonised", "topics": [ "isHarmonised", "isHarmonised,DataSet-method" ] }, { "page": "isHarmonisedLD-methods", "title": "Check if the DataSet is harmonised against LD matrix", "topics": [ "isHarmonisedLD", "isHarmonisedLD,DataSet-method" ] }, { "page": "lbf_to_z_cont", "title": "Convert log Bayes Factor to summary stats", "topics": [ "lbf_to_z_cont" ] }, { "page": "ld_matrix_local", "title": "modified from ieugwasr::ld_matrix_local () Get LD matrix using local plink binary and reference dataset", "topics": [ "ld_matrix_local" ] }, { "page": "liftover", "title": "Remap genomic coordinates to a different genome assembly", "topics": [ "liftover" ] }, { "page": "merge_datasets", "title": "Merge Datasets", "topics": [ "merge_datasets" ] }, { "page": "meta_analysis", "title": "Meta analysis", "topics": [ "meta_analysis" ] }, { "page": "overlapVariants-methods", "title": "Look for overlapped variants between SummarySets in the DataSet and Resize", "topics": [ "overlapVariants", "overlapVariants,DataSet-method" ] }, { "page": "plot_gwasglue", "title": "Plot", "topics": [ "plot_gwasglue" ] }, { "page": "setAttributes-methods", "title": "Set Method to store the attributes of the SummarySet", "topics": [ "setAttributes", "setAttributes,SummarySet-method" ] }, { "page": "setMetadata-methods", "title": "Set Method to add metadata to the SummarySet", "topics": [ "setMetadata", "setMetadata,SummarySet-method" ] }, { "page": "setRSID-methods", "title": "Set Method to store RSID/variants in the SummarySet", "topics": [ "setRSID", "setRSID,SummarySet-method" ] }, { "page": "setShape-methods", "title": "Set the Shape of the gwasglue2 objects", "topics": [ "setShape", "setShape,SummarySet-method" ] }, { "page": "setTraitOrg-methods", "title": "Set the trait organisation of the gwasglue2 DataSet", "topics": [ "setTraitOrg", "setTraitOrg,DataSet-method" ] }, { "page": "setVariantid-methods", "title": "Set Method to create an internal Variant ID for the SummarySet", "topics": [ "setVariantid", "setVariantid,SummarySet-method" ] }, { "page": "setVariants-methods", "title": "Set Method to store RSID/variants in the SummarySet", "topics": [ "setVariants", "setVariants,SummarySet-method" ] }, { "page": "setZscores-methods", "title": "Calculating Z-scores", "topics": [ "setZscores", "setZscores,DataSet-method" ] }, { "page": "SummarySet-class", "title": "An S4 class to represent the Summary Set", "topics": [ "SummarySet-class" ] }, { "page": "susie_to_dataset", "title": "SusieR to DataSet", "topics": [ "susie_to_dataset" ] } ], "_readme": "https://github.com/MRCIEU/gwasglue2/raw/HEAD/README.md", "_rundeps": [ "cli", "dplyr", "generics", "glue", "lifecycle", "magrittr", "pillar", "pkgconfig", "R6", "rlang", "tibble", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "Strategy.Rmd", "filename": "Strategy.html", "title": "Strategy", "engine": "knitr::rmarkdown", "headings": [ "Objectives", "Data structures", "Work flow", "Strategy", "Implementation", "Controlled fields", "Design", "Variantid" ], "created": "2022-11-23 15:15:40", "modified": "2023-07-17 16:09:44", "commits": 4 }, { "source": "SummarySet_DataSet.Rmd", "filename": "SummarySet_DataSet.html", "title": "Tutorial 1: How to create a SummarySet and a DataSet", "engine": "knitr::rmarkdown", "headings": [ "SummarySet", "Create a Summaryset from a GWAS vcf file", "DataSet" ], "created": "2023-07-17 16:09:44", "modified": "2023-09-12 16:41:56", "commits": 4 }, { "source": "mr.Rmd", "filename": "mr.html", "title": "Tutorial 2: MR analysis", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-06-27 10:04:26", "modified": "2023-07-17 16:09:44", "commits": 2 }, { "source": "finemap_coloc1.Rmd", "filename": "finemap_coloc1.html", "title": "Tutorial 3: Regional genotype-phenotype map", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-06-27 10:04:26", "modified": "2023-07-17 16:09:44", "commits": 2 }, { "source": "meta.Rmd", "filename": "meta.html", "title": "Tutorial 4: Meta analysis", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-06-13 15:50:58", "modified": "2023-08-03 19:43:02", "commits": 5 }, { "source": "finemap_coloc2.Rmd", "filename": "finemap_coloc2.html", "title": "Tutorial 5: Alternative regional genotype-phenotype map example, with meta-analyses included", "engine": "knitr::rmarkdown", "headings": [ "1. Setting the metadata", "2. HMGCR (3-hydroxy-3-methylglutaryl-CoA reductase) gene region", "2.1. Meta-analysis for the chd trait", "2.2. Creating a dataset for all the traits", "2.3. Finemapping with SusieR", "2.4. Colocolisation with hypercoloc", "3. PCSK9 (proprotein convertase subtilisin/kexin type 9) gene region", "3.1. Meta-analysis for the chd trait", "3.2. Creating a dataset for all the traits", "3.3. Finemapping with SusieR", "3.4. Colocolisation with hypercoloc", "4. NPC1L1 (NPC1 like intracellular cholesterol transporter 1) gene region", "4.1. Meta-analysis for the chd trait", "4.2. Creating a dataset for all the traits", "4.3. Finemapping with SusieR", "4.4. Colocolisation with hypercoloc", "5. LPA (Lipoprotein(A)) gene region", "5.1. Meta-analysis for the chd trait", "5.2. Creating a dataset for all the traits", "5.3. Finemapping with SusieR", "5.4. Colocolisation with hypercoloc" ], "created": "2023-06-27 10:04:26", "modified": "2023-08-03 19:43:02", "commits": 3 }, { "source": "liftover.Rmd", "filename": "liftover.html", "title": "Tutorial 6: Remap genomic coordinates to a different genome assembly", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-08-03 19:43:02", "modified": "2023-08-08 14:25:19", "commits": 2 } ], "_score": 5.462098381135156, "_indexed": true, "_nocasepkg": "gwasglue2", "_universes": [ "mrcieu", "ritarasteiro" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.0.9000", "date": "2026-05-20T09:32:30.000Z", "distro": "noble", "commit": "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "fileid": "e7722d3124701b2067b3663d48919ad82bbb42a12598b793dfcc3c6501384d25", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26153676913" }, { "r": "4.6.0", "os": "linux", "version": "0.0.0.9000", "date": "2026-05-20T09:32:35.000Z", "distro": "noble", "commit": "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "fileid": "be2b1baee71e955dff42205d3f184650e3d96c89cf36f5679639a98db25f2da4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26153676913" }, { "r": "4.5.3", "os": "mac", "version": "0.0.0.9000", "date": "2026-05-20T09:31:32.000Z", "commit": "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "fileid": "2a04aec224230cb5800b90755adeaac819ce40b69b5d075fcebd60e38f8fe32b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26153676913" }, { "r": "4.6.0", "os": "mac", "version": "0.0.0.9000", "date": "2026-05-20T09:31:19.000Z", "commit": "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "fileid": "74f510896c241e8546c7b2a89f6d981cf249c6d870dc3168f2552c7986763de5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26153676913" }, { "r": "4.7.0", "os": "win", "version": "0.0.0.9000", "date": "2026-05-20T09:31:22.000Z", "commit": "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "fileid": "7f3bb482a3a078b84418c0097d9bf07532b0b94164d5a1e4205c3f93a3418946", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26153676913" }, { "r": "4.5.3", "os": "win", "version": "0.0.0.9000", "date": "2026-05-20T09:33:53.000Z", "commit": "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "fileid": "887214ffd3de77eaba0dec437d4f9e29563d7a73bea76d4b8673e513f299eba4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26153676913" }, { "r": "4.6.0", "os": "win", "version": "0.0.0.9000", "date": "2026-05-20T09:31:28.000Z", "commit": "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "fileid": "3bfb9814c8bf3223934bcd6b78a35e2688ef5e06bd55d4b868dc00201882e5ab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26153676913" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.0.9000", "date": "2026-06-02T13:21:56.000Z", "commit": "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "fileid": "eb365b015b0d5ec611878f5a86a4a029656a22065ce6463717fc49183d11a909", "status": "success", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26153676913" } ] }