{ "_id": "6a194cdeacfb0bcc41ddd981", "Package": "ldblock", "Title": "data structures for linkage disequilibrium measures in\npopulations", "Version": "1.42.0", "Author": "VJ Carey ", "Description": "Define data structures for linkage disequilibrium measures\nin populations.", "Maintainer": "VJ Carey ", "License": "Artistic-2.0", "LazyData": "no", "BiocViews": "genetics, SNP, GWAS, LinkageDisequilibrium", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:41:47 UTC", "RemoteUrl": "https://github.com/bioc/ldblock", "RemoteRef": "RELEASE_3_23", "RemoteSha": "24b436b381173d91c58b6ca897c1c98761e40ba8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:16:48 UTC", "User": "root" }, "MD5sum": "9f2671f754b1161098b134a7c2c7c384", "_user": "bioc-release", "_type": "src", "_file": "ldblock_1.42.0.tar.gz", "_fileid": "e8bd832823f60606cb3aa178831d5cb9ec7eddc84ad0aa8c10f2eb3be0ca64b9", "_filesize": 41935166, "_sha256": "e8bd832823f60606cb3aa178831d5cb9ec7eddc84ad0aa8c10f2eb3be0ca64b9", "_created": "2026-05-29T07:16:48.000Z", "_published": "2026-05-29T08:22:53.986Z", "_jobs": [ { "job": 78455686062, "time": 223, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7285262258" }, { "job": 78455686069, "time": 327, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7285290364" }, { "job": 78455686058, "time": 340, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7285294379" }, { "job": 78455686090, "time": 138, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7286301613" }, { "job": 78455686143, "time": 183, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7286314533" }, { "job": 78455014137, "time": 309, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285201313" }, { "job": 78455686071, "time": 184, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285251240" }, { "job": 78455686101, "time": 200, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7285255990" }, { "job": 78455686083, "time": 218, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7285261310" }, { "job": 78455686097, "time": 197, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7285254704" } ], "_bioccheck": { "error": 2, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623601175", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ldblock", "_commit": { "id": "24b436b381173d91c58b6ca897c1c98761e40ba8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380107 }, "_maintainer": { "name": "VJ Carey", "email": "stvjc@channing.harvard.edu", "login": "vjcitn", "description": "Professor of Medicine, Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School.", "uuid": 4624066 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "rlang", "role": "Depends" }, { "package": "BiocGenerics", "version": ">= 0.25.1", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "RUnit", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "gwascat", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "snpStats", "role": "Suggests" }, { "package": "VariantAnnotation", "role": "Suggests" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "ensembldb", "role": "Suggests" }, { "package": "EnsDb.Hsapiens.v75", "role": "Suggests" }, { "package": "Rsamtools", "role": "Suggests" }, { "package": "GenomicFiles", "version": ">= 1.13.6", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-31", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.43.0", "bioc": "3.24" }, { "branch": "release", "version": "1.42.0", "bioc": "3.23" } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 544, "source": "https://www.bioconductor.org/packages/stats/bioc/ldblock" }, "_mentions": 1, "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ldblock.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "downloadPopByChr", "expandSnpSet", "hmld", "ldByGene", "ldmat", "s3_1kg", "stack1kg" ], "_datasets": [ { "name": "EUR_singletons", "title": "singletons from EUR", "object": "EUR_singletons", "file": "EUR_singletons.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "sampinf_1kg", "title": "population and relationship information for 1000 genomes", "object": "sampinf_1kg", "file": "sampinf_1kg.rda", "class": [ "data.frame" ], "fields": [ "Sample", "Family.ID", "Population", "Population.Description", "Gender", "Relationship", "Unexpected.Parent.Child", "Non.Paternity", "Siblings", "Grandparents", "Avuncular", "Half.Siblings", "Unknown.Second.Order", "Third.Order", "Other.Comments", "superpop" ], "rows": 3500, "table": true, "tojson": true } ], "_help": [ { "page": "ldblock-package", "title": "c(\"\\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\\\"#1\\\")\", \"ldblock\")data structures for linkage disequilibrium measures in populations", "topics": [ "ldblock-package", "ldblock" ] }, { "page": "downloadPopByChr", "title": "download hapmap resource with LD estimates", "topics": [ "downloadPopByChr" ] }, { "page": "EUR_singletons", "title": "singletons from EUR", "topics": [ "EUR_singletons" ] }, { "page": "expandSnpSet", "title": "Given a set of SNP identifiers, use LD to expand the set to include linked loci", "topics": [ "expandSnpSet" ] }, { "page": "hmld", "title": "import hapmap LD data and create a structure for its management; generates a sparse matrix representation of pairwise LD statistics and binds metadata on variant name and position", "topics": [ "hmld" ] }, { "page": "ldByGene", "title": "Obtain LD statistics in region specified by a gene model.", "topics": [ "ldByGene" ] }, { "page": "ldmat", "title": "use LDmat API from NCI LDlink service", "topics": [ "ldmat" ] }, { "page": "ldmat-ldstruct-method", "title": "accessor for matrix component", "topics": [ "ldmat,ldstruct-method" ] }, { "page": "ldstruct-class", "title": "container for LD data", "topics": [ "ldstruct-class" ] }, { "page": "s3_1kg", "title": "Create a URL referencing 1000 genomes content in AWS S3. stack1kg produces a VcfStack instance with references to VCF for 1000 genomes autosomal chrs. S3-resident VCF files with version \"v5a.20130502\" are used.", "topics": [ "s3_1kg" ] }, { "page": "sampinf_1kg", "title": "population and relationship information for 1000 genomes", "topics": [ "sampinf_1kg" ] }, { "page": "stack1kg", "title": "couple together a group of VCFs", "topics": [ "stack1kg" ] } ], "_rundeps": [ "askpass", "BiocGenerics", "curl", "generics", "httr", "IRanges", "jsonlite", "lattice", "Matrix", "mime", "openssl", "R6", "rlang", "S4Vectors", "Seqinfo", "sys" ], "_vignettes": [ { "source": "ldblock.Rmd", "filename": "ldblock.html", "title": "ldblock package: linkage disequilibrium data structures", "author": "Vincent J. Carey, stvjc at channing.harvard.edu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Import of HapMap LD data", "A view of the block structure", "Collecting SNPs exhibiting linkage to selected SNP" ], "created": "2015-03-09 07:19:30", "modified": "2020-06-30 13:24:16", "commits": 9 } ], "_score": 3.653212513775344, "_indexed": false, "_nocasepkg": "ldblock", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/ldblock", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.42.0", "date": "2026-05-29T07:21:15.000Z", "distro": "noble", "commit": "24b436b381173d91c58b6ca897c1c98761e40ba8", "fileid": "873608f3062c9e2cc97b70413dac13fb4817a25b3530e1eed673dbb21b98c9a5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623601175" }, { "r": "4.6.0", "os": "linux", "version": "1.42.0", "date": "2026-05-29T07:21:31.000Z", "distro": "noble", "commit": "24b436b381173d91c58b6ca897c1c98761e40ba8", "fileid": "c7c3b33b0c7156cf21bdfe00c5b1598b1e2d8857f273af26b470a0263b22fdb2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623601175" }, { "r": "4.5.3", "os": "mac", "version": "1.42.0", "date": "2026-05-29T08:20:55.000Z", "commit": "24b436b381173d91c58b6ca897c1c98761e40ba8", "fileid": "cda2a864f9bbbc04a5fad46153796a6b9d56ab82ac397d01857239b436acec0b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623601175" }, { "r": "4.6.0", "os": "mac", "version": "1.42.0", "date": "2026-05-29T08:21:30.000Z", "commit": "24b436b381173d91c58b6ca897c1c98761e40ba8", "fileid": "f3d8c0b015959f64052291ca61d13977ae525abbb4421313591efd60eb81524b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623601175" }, { "r": "4.6.0", "os": "wasm", "version": "1.42.0", "date": "2026-05-29T07:20:14.000Z", "commit": "24b436b381173d91c58b6ca897c1c98761e40ba8", "fileid": "6ba8b2689c1a61da9565553ff723a0bb68357d99bba3a79bf9f8429eaa856394", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623601175" }, { "r": "4.7.0", "os": "win", "version": "1.42.0", "date": "2026-05-29T07:19:20.000Z", "commit": "24b436b381173d91c58b6ca897c1c98761e40ba8", "fileid": "96f78fac85db2c842b856724b0468c7f323ea366baccfd31fbbdd1979997fc3c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623601175" }, { "r": "4.5.3", "os": "win", "version": "1.42.0", "date": "2026-05-29T07:19:27.000Z", "commit": "24b436b381173d91c58b6ca897c1c98761e40ba8", "fileid": "70dc9f8c332548f4be44010542142ea7de3023e019facaf3b44e3d179f2c8973", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623601175" }, { "r": "4.6.0", "os": "win", "version": "1.42.0", "date": "2026-05-29T07:19:09.000Z", "commit": "24b436b381173d91c58b6ca897c1c98761e40ba8", "fileid": "3da1e765aa732ab5189098b6eda285bc1ddd6e56ec0a0ab1882c27161cf8440d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623601175" } ] }