{ "_id": "6a49415b18cdde069385dfe6", "Package": "PlinkMatrix", "Title": "DelayedArray interface for plink bed files", "Version": "1.1.0", "Authors@R": "c(person(given = \"Vince\",\nfamily = \"Carey\",\nrole = c(\"aut\", \"cre\"),\nemail = \"stvjc@channing.harvard.edu\",\ncomment = c(ORCID = \"0000-0003-4046-0063\")),\nperson(\"NHGRI U24HG004059\", role=\"fnd\"))", "Description": "This package provides a DelayedArray interface for plink\nbed files. There is support for interfacing to plink genotype\ndata via RangedSummarizedExperiment. Example data from the\nGEUVADIS project (internationalgenome.org) are used for\ndemonstration.", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "biocViews": "Infrastructure, Genetics", "Encoding": "UTF-8", "URL": "https://github.com/vjcitn/PlinkMatrix", "BugReports": "https://github.com/vjcitn/PlinkMatrix/issues", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libicu-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:06:58 UTC", "RemoteUrl": "https://github.com/bioc/PlinkMatrix", "RemoteRef": "HEAD", "RemoteSha": "bfa6bf024320391550fbb2445069b7ce809247a4", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-04 07:54:43 UTC", "User": "root" }, "Author": "Vince Carey [aut, cre] (ORCID: ),\nNHGRI U24HG004059 [fnd]", "Maintainer": "Vince Carey ", "_user": "bioc", "_type": "src", "_file": "PlinkMatrix_1.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/59f17a976ad6bf60ca0003368a929e37d0d1d19542bda7e61202e7f1c62edcc4", "_filesize": 2084160, "_sha256": "59f17a976ad6bf60ca0003368a929e37d0d1d19542bda7e61202e7f1c62edcc4", "_expires": "2026-10-12T17:22:33.000Z", "_created": "2026-07-04T07:54:43.000Z", "_published": "2026-07-04T17:22:35.657Z", "_bioccheck": { "error": 0, "warning": 0, "note": 2 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576", "_status": "success", "_upstream": "https://github.com/bioc/PlinkMatrix", "_commit": { "id": "bfa6bf024320391550fbb2445069b7ce809247a4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381618 }, "_maintainer": { "name": "Vince 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, "orcid": "0000-0003-4046-0063" }, "_distro": "resolute", "_jobs": [ { "job": 85151816408, "time": 181, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8079820876" }, { "job": 85151816471, "time": 283, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "8079833403" }, { "job": 85151816377, "time": 329, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8079838940" }, { "job": 85151816443, "time": 363, "config": "linux-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8079843943" }, { "job": 85151816542, "time": 343, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8079840719" }, { "job": 85151816448, "time": 215, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8080160431" }, { "job": 85151816407, "time": 306, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "8079836916" }, { "job": 85151816436, "time": 172, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8080161905" }, { "job": 85151816362, "time": 409, "config": "macos-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8079850254" }, { "job": 85151816227, "time": 266, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8079800180" }, { "job": 85151816470, "time": 159, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8079818309" }, { "job": 85151816426, "time": 293, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8079834302" }, { "job": 85151816358, "time": 207, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8079824058" }, { "job": 85151816450, "time": 245, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8079828747" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Rcpp", "role": "Depends" }, { "package": "DelayedArray", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "irlba", "role": "Suggests" }, { "package": "GenomeInfoDb", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-01", "n": 5 }, { "week": "2026-03", "n": 1 }, { "week": "2026-04", "n": 5 }, { "week": "2026-07", "n": 9 }, { "week": "2026-08", "n": 1 }, { "week": "2026-11", "n": 2 }, { "week": "2026-14", "n": 5 }, { "week": "2026-15", "n": 7 }, { "week": "2026-16", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.1.0", "bioc": "3.24" }, { "branch": "release", "version": "1.0.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "genetics", "cpp" ], "_stars": 1, "_contributors": [ { "user": "vjcitn", "count": 36, "uuid": 4624066 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/vjcitn/plinkmatrix", "_searchresults": 10, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PlinkMatrix.html", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/vjcitn/plinkmatrix", "_realowner": "bioc", "_cranurl": false, "_exports": [ "example_PlinkMatrix", "get_plink_example_path", "getSampleData", "getVariantData", "plid2gr", "PlinkMatrix", "PlinkSeed", "read_bed_subset", "show" ], "_datasets": [ { "name": "example_GRanges", "title": "sample GRanges coordinated with example_PlinkMatrix", "object": "example_GRanges", "file": "example_GRanges.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "g445samples", "title": "sample characteristics of 445 GEUVADIS samples", "object": "g445samples", "file": "g445samples.rda", "class": [ "data.frame" ], "fields": [ "Sex", "Population.code", "Population.name", "Superpopulation.code", "Superpopulation.name" ], "rows": 445, "table": true, "tojson": true } ], "_help": [ { "page": "dim-PlinkSeed-method", "title": "Method: dim for delayed plink", "topics": [ "dim,PlinkSeed-method" ] }, { "page": "dimnames-PlinkSeed-method", "title": "Method: dimnames for delayed plink", "topics": [ "dimnames,PlinkSeed-method" ] }, { "page": "example_GRanges", "title": "sample GRanges coordinated with example_PlinkMatrix", "topics": [ "example_GRanges" ] }, { "page": "example_PlinkMatrix", "title": "produce PlinkMatrix from example data", "topics": [ "example_PlinkMatrix" ] }, { "page": "g445samples", "title": "sample characteristics of 445 GEUVADIS samples", "topics": [ "g445samples" ] }, { "page": "get_plink_example_path", "title": "operate with BiocFileCache to retrieve zip file of plink example data", "topics": [ "get_plink_example_path" ] }, { "page": "getSampleData", "title": "Get sample metadata", "topics": [ "getSampleData" ] }, { "page": "getVariantData", "title": "Get variant metadata", "topics": [ "getVariantData" ] }, { "page": "plid2gr", "title": "produce GRanges from variant notation for plink example from geuvadis", "topics": [ "plid2gr" ] }, { "page": "PlinkMatrix", "title": "Constructor for DelayedArray", "topics": [ "PlinkMatrix" ] }, { "page": "PlinkMatrix-pkg", "title": "Delayed interface to Plink genotype files", "topics": [ "PlinkMatrix-pkg" ] }, { "page": "read_bed_subset", "title": "read subset for use in delayed matrix approach", "topics": [ "read_bed_subset" ] }, { "page": "show-PlinkSeed-method", "title": "present seed concisely", "topics": [ "show,PlinkSeed-method" ] } ], "_readme": "https://github.com/bioc/PlinkMatrix/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "Biobase", "BiocFileCache", "BiocGenerics", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "fastmap", "filelock", "generics", "GenomicRanges", "glue", "httr2", "IRanges", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "openssl", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "Rcpp", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "PlinkMatrix.Rmd", "filename": "PlinkMatrix.html", "title": "PlinkMatrix: DelayedArray interface to plink bed-type files", "author": "Vincent J. Carey, stvjc at channing.harvard.edu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Demonstration", "Sanity check", "SummarizedExperiment wrapper; subsetting with GenomicRanges", "Session information" ], "created": "2026-02-09 23:08:52", "modified": "2026-04-06 10:18:33", "commits": 7 } ], "_score": 4.698970004336019, "_indexed": true, "_nocasepkg": "plinkmatrix", "_universes": [ "bioc", "vjcitn" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-07-04T07:58:15.000Z", "distro": "resolute", "arch": "aarch64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/5e668dfb20bfef5c7313efdf40fb627fefdf8671a38e8d41d6842277ebc3b2db", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-07-04T07:58:10.000Z", "distro": "resolute", "arch": "x86_64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/9fdf8091dbb864fae2dc023fcc9c39a7a06c34d79351e843d1efa63651d560a8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.6.1", "os": "linux", "version": "1.1.0", "date": "2026-07-04T07:58:28.000Z", "distro": "resolute", "arch": "aarch64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/db23b1cfe4e3162a02e948f10d2ce04f402ae3c7bea4646bebbbc0a1ea2fdd97", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.6.1", "os": "linux", "version": "1.1.0", "date": "2026-07-04T07:58:36.000Z", "distro": "resolute", "arch": "x86_64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/56f2f5652cab584f1d989eeb06817aa4cc80fa8802de7c43782b594f1555bdbd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-07-04T08:44:11.000Z", "arch": "aarch64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/5e55548eeba904011138ccb2cc3ce195d1fc84e059acbd871ec2c863c76425b5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-07-04T07:57:31.000Z", "arch": "x86_64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/1c31c29bc6f2eb4878e9c8be81f29b3337d201ebae9133a1dd7215e5d618debb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.6.1", "os": "mac", "version": "1.1.0", "date": "2026-07-04T08:45:06.000Z", "arch": "aarch64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/39d9d3ce7cc90d570d70d4712c803fb57e210c5b88fd03c6297b1285782145c1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.6.1", "os": "mac", "version": "1.1.0", "date": "2026-07-04T07:58:45.000Z", "arch": "x86_64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/e2cda8d19ee116ac41a4f8a0337fd745d6894ee7000daa5bb75d99ae7e8a4994", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-07-04T07:57:53.000Z", "arch": "emscripten", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/a71c68895fbd44e81fa3d6ec6030be904381c4eac3ed0839eea8a6d13eeb3f31", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-07-04T07:56:59.000Z", "arch": "x86_64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/ce12c91a0ff6fb51796be0a3d84bfa164a027965b63bbe1d6522dedac99db0b5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.5.3", "os": "win", "version": "1.1.0", "date": "2026-07-04T07:56:21.000Z", "arch": "x86_64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/caca36ebd838e51403e3aada2dae1a28f6e85ae99793ea529132aa395454349d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" }, { "r": "4.6.1", "os": "win", "version": "1.1.0", "date": "2026-07-04T07:56:20.000Z", "arch": "x86_64", "commit": "bfa6bf024320391550fbb2445069b7ce809247a4", "fileid": "https://r2.ropensci.org/cb80e813dcd1573f21806e3232fad5e238d48d83b9acb2f2488b0b9888e09faa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699649576" } ] }