{ "_id": "6ac0d7f891601a2ad29997bd", "Package": "genio", "Title": "Genetics Input/Output Functions", "Version": "1.1.6.9000", "Authors@R": "person(given = \"Alejandro\",\nfamily = \"Ochoa\",\nrole = c(\"aut\", \"cre\"),\nemail = \"alejandro.ochoa@duke.edu\",\ncomment = c(ORCID = \"0000-0003-4928-3403\"))", "Description": "Implements readers and writers for file formats associated\nwith genetics data. Reading and writing Plink BED/BIM/FAM and\nGCTA binary GRM formats is fully supported, including a\nlightning-fast BED reader and writer implementations. Other\nfunctions are 'readr' wrappers that are more constrained,\nuser-friendly, and efficient for these particular applications;\nhandles Plink and Eigenstrat tables (FAM, BIM, IND, and SNP\nfiles). There are also make functions for FAM and BIM tables\nwith default values to go with simulated genotype data.", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "URL": "https://github.com/OchoaLab/genio", "BugReports": "https://github.com/OchoaLab/genio/issues", "Config/pak/sysreqs": "libx11-dev", "Repository": "https://ochoalab.r-universe.dev", "Date/Publication": "2025-02-20 22:53:41 UTC", "RemoteUrl": "https://github.com/ochoalab/genio", "RemoteRef": "HEAD", "RemoteSha": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-03 10:18:10 UTC", "User": "root" }, "Author": "Alejandro Ochoa [aut, cre] (ORCID:\n)", "Maintainer": "Alejandro Ochoa ", "_user": "ochoalab", "_type": "src", "_file": "genio_1.1.6.9000.tar.gz", "_fileid": "https://r2.ropensci.org/f21b2267cb552de7ae97d78a84905ccddbe3945254c573aedb8783cbdfa4ab2d", "_filesize": 786586, "_sha256": "f21b2267cb552de7ae97d78a84905ccddbe3945254c573aedb8783cbdfa4ab2d", "_expires": "2027-01-11T10:24:54.000Z", "_created": "2026-10-03T10:18:10.000Z", "_published": "2026-10-03T10:24:56.561Z", "_jobs": [ { "job": 111182801044, "time": 109, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11271481288" }, { "job": 111182801102, "time": 141, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11271471274" }, { "job": 111182800975, "time": 150, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11271471286" }, { "job": 111182801016, "time": 127, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11272110213" }, { "job": 111182801019, "time": 159, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "11271581101" }, { "job": 111182801021, "time": 266, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "11271995617" }, { "job": 111182801015, "time": 138, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "11271446458" }, { "job": 111182801048, "time": 232, "config": "macos-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "11270419717" }, { "job": 111182207021, "time": 219, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11270194966" }, { "job": 111182800979, "time": 101, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11272005355" }, { "job": 111182801043, "time": 359, "config": "windows-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "11272085625" }, { "job": 111182801057, "time": 153, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "11272135281" }, { "job": 111182801061, "time": 112, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "11271416523" }, { "job": 111182801076, "time": 312, "config": "windows-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "11271990676" }, { "job": 111182801105, "time": 101, "config": "windows-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "11271665795" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922", "_status": "success", "_upstream": "https://github.com/ochoalab/genio", "_commit": { "id": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "author": "Alejandro Ochoa Garcia ", "committer": "Alejandro Ochoa Garcia ", "message": "Internal function `add_ext_read` (affects `count_lines`, `het_reencode_bed`, and probably all or most `read_*` functions) now works as intended when the file without extension matches a directory name, so that the directory is ignored and the extension is added as expected\n", "time": 1740092021 }, "_maintainer": { "name": "Alejandro Ochoa", "email": "alejandro.ochoa@duke.edu", "login": "alexviiia", "orcid": "0000-0003-4928-3403", "description": "Statistical geneticist, computational biologist. Well-rounded nerd, also love languages and music.", "uuid": 12603341 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "readr", "version": ">= 2.0.0", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "R.utils", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BEDMatrix", "role": "Suggests" }, { "package": "snpStats", "role": "Suggests" }, { "package": "lobstr", "role": "Suggests" } ], "_owner": "ochoalab", "_selfowned": true, "_usedby": 6, "_updates": [], "_tags": [], "_stars": 19, "_contributors": [ { "user": "alexviiia", "count": 104, "uuid": 12603341 } ], "_userbio": { "uuid": 41968176, "type": "organization", "name": "Ochoa Lab at Duke StatGen", "followers": 7, "description": "Research in statgen, biostats, compbio" }, "_downloads": { "count": 1085, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/genio" }, "_devurl": "https://github.com/ochoalab/genio", "_searchresults": 434, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/genio.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/ochoalab/genio", "_realowner": "ochoalab", "_cranurl": true, "_releases": [ { "version": "1.0.9", "date": "2019-05-24" }, { "version": "1.0.10", "date": "2019-05-28" }, { "version": "1.0.12", "date": "2019-12-17" }, { "version": "1.0.23", "date": "2021-06-11" }, { "version": "1.0.25", "date": "2021-07-26" }, { "version": "1.1.1", "date": "2022-04-27" }, { "version": "1.1.2", "date": "2023-01-07" } ], "_exports": [ "count_lines", "delete_files_grm", "delete_files_phen", "delete_files_plink", "geno_to_char", "het_reencode_bed", "ind_to_fam", "make_bim", "make_fam", "read_bed", "read_bim", "read_eigenvec", "read_fam", "read_grm", "read_ind", "read_matrix", "read_phen", "read_plink", "read_snp", "require_files_grm", "require_files_phen", "require_files_plink", "sex_to_char", "sex_to_int", "sim_and_write_plink", "symlink", "tidy_kinship", "write_bed", "write_bim", "write_eigenvec", "write_fam", "write_grm", "write_ind", "write_matrix", "write_phen", "write_plink", "write_snp" ], "_help": [ { "page": "count_lines", "title": "Count the number of lines of a file", "topics": [ "count_lines" ] }, { "page": "delete_files_grm", "title": "Delete all GCTA binary GRM files", "topics": [ "delete_files_grm" ] }, { "page": "delete_files_phen", "title": "Delete PHEN files", "topics": [ "delete_files_phen" ] }, { "page": "delete_files_plink", "title": "Delete all Plink binary files", "topics": [ "delete_files_plink" ] }, { "page": "genio", "title": "genio (GENetics I/O): A package for reading and writing genetics data", "topics": [ "genio-package", "genio" ] }, { "page": "geno_to_char", "title": "Convert a genotype matrix from numeric to character codes", "topics": [ "geno_to_char" ] }, { "page": "het_reencode_bed", "title": "Reencode a Plink BED file to (twice) heterozygote indicators", "topics": [ "het_reencode_bed" ] }, { "page": "ind_to_fam", "title": "Convert an Eigenstrat IND tibble into a Plink FAM tibble", "topics": [ "ind_to_fam" ] }, { "page": "make_bim", "title": "Create a Plink BIM tibble", "topics": [ "make_bim" ] }, { "page": "make_fam", "title": "Create a Plink FAM tibble", "topics": [ "make_fam" ] }, { "page": "read_bed", "title": "Read a genotype matrix in Plink BED format", "topics": [ "read_bed" ] }, { "page": "read_bim", "title": "Read Plink *.bim files", "topics": [ "read_bim" ] }, { "page": "read_eigenvec", "title": "Read Plink eigenvec file", "topics": [ "read_eigenvec" ] }, { "page": "read_fam", "title": "Read Plink *.fam files", "topics": [ "read_fam" ] }, { "page": "read_grm", "title": "Read GCTA GRM and related plink2 binary files", "topics": [ "read_grm" ] }, { "page": "read_ind", "title": "Read Eigenstrat *.ind files", "topics": [ "read_ind" ] }, { "page": "read_matrix", "title": "Read a numerical matrix file into an R matrix", "topics": [ "read_matrix" ] }, { "page": "read_phen", "title": "Read *.phen files", "topics": [ "read_phen" ] }, { "page": "read_plink", "title": "Read genotype and sample data in a Plink BED/BIM/FAM file set.", "topics": [ "read_plink" ] }, { "page": "read_snp", "title": "Read Eigenstrat *.snp files", "topics": [ "read_snp" ] }, { "page": "require_files_grm", "title": "Require that GCTA binary GRM files are present", "topics": [ "require_files_grm" ] }, { "page": "require_files_phen", "title": "Require that PHEN file is present", "topics": [ "require_files_phen" ] }, { "page": "require_files_plink", "title": "Require that Plink binary files are present", "topics": [ "require_files_plink" ] }, { "page": "sex_to_char", "title": "Convert integer sex codes to character codes", "topics": [ "sex_to_char" ] }, { "page": "sex_to_int", "title": "Convert character sex codes to integer codes", "topics": [ "sex_to_int" ] }, { "page": "sim_and_write_plink", "title": "Simulate and write genotypes to plink format on the fly", "topics": [ "sim_and_write_plink" ] }, { "page": "symlink", "title": "Create a symbolic link to a file, adjusting paths automatically if needed", "topics": [ "symlink" ] }, { "page": "tidy_kinship", "title": "Create a tidy version of a kinship matrix", "topics": [ "tidy_kinship" ] }, { "page": "write_bed", "title": "Write a genotype matrix into Plink BED format", "topics": [ "write_bed" ] }, { "page": "write_bim", "title": "Write Plink *.bim files", "topics": [ "write_bim" ] }, { "page": "write_eigenvec", "title": "Write eigenvectors table into a Plink-format file", "topics": [ "write_eigenvec" ] }, { "page": "write_fam", "title": "Write Plink *.fam files", "topics": [ "write_fam" ] }, { "page": "write_grm", "title": "Write GCTA GRM and related plink2 binary files", "topics": [ "write_grm" ] }, { "page": "write_ind", "title": "Write Eigenstrat *.ind files", "topics": [ "write_ind" ] }, { "page": "write_matrix", "title": "Write a matrix to a file without row or column names", "topics": [ "write_matrix" ] }, { "page": "write_phen", "title": "Write *.phen files", "topics": [ "write_phen" ] }, { "page": "write_plink", "title": "Write genotype and sample data into a Plink BED/BIM/FAM file set.", "topics": [ "write_plink" ] }, { "page": "write_snp", "title": "Write Eigenstrat *.snp files", "topics": [ "write_snp" ] } ], "_pkglogo": "https://github.com/ochoalab/genio/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/ochoalab/genio/raw/HEAD/README.md", "_rundeps": [ "bit", "bit64", "cli", "clipr", "cpp11", "crayon", "dplyr", "generics", "glue", "hms", "lifecycle", "magrittr", "pillar", "pkgconfig", "prettyunits", "progress", "R.methodsS3", "R.oo", "R.utils", "R6", "Rcpp", "readr", "rlang", "tibble", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr" ], "_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": "genio.Rmd", "filename": "genio.html", "title": "Read and write BED files with genio", "author": "Alejandro Ochoa", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Generate a large matrix of random genotypes", "Write genotypes to Plink files", "Read back the genotypes", "Memory estimation", "Comparison to other packages", "BEDMatrix", "snpStats", "Overall time comparisons", "Memory comparison", "Cleanup" ], "created": "2019-05-17 04:07:33", "modified": "2021-07-26 21:46:29", "commits": 12 } ], "_score": 7.905915578089212, "_indexed": true, "_nocasepkg": "genio", "_universes": [ "ochoalab", "alexviiia" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.6.9000", "date": "2026-10-03T10:20:03.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/451bd841c3e5202db61bc0b22fa6d177bfcf77988250772336b61bc85034b872", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.7.0", "os": "linux", "version": "1.1.6.9000", "date": "2026-10-03T10:20:24.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/0675f96082513e477bbcfa24d651f6539f8f102c1376f7777ceafc7970635c5e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.6.1", "os": "linux", "version": "1.1.6.9000", "date": "2026-10-03T10:20:46.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/10f38e7d15ce1b7b0e839feaa8f0391a18e8b3ea0505b15f348802f3514a6c5c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.6.1", "os": "linux", "version": "1.1.6.9000", "date": "2026-10-03T10:20:16.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/939709fcd4f80aad879712f42d865b9b4ba53a20ed8a1d13ffa81b0535cc2b82", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.5.3", "os": "mac", "version": "1.1.6.9000", "date": "2026-10-03T10:20:44.000Z", "arch": "aarch64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/de165f6d76cdd95a09b9de435f09ccd225f3bedc8d66dca7643a563b75956373", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.5.3", "os": "mac", "version": "1.1.6.9000", "date": "2026-10-03T10:22:05.000Z", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/4aefcabc023b50bd033fae3a4d8658ef3c2861f349d220a612a691f771833c89", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.6.1", "os": "mac", "version": "1.1.6.9000", "date": "2026-10-03T10:20:36.000Z", "arch": "aarch64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/2bf10b6216674150c70e4761504039649a6b541ab671099a6ac79d06b1f92551", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.6.1", "os": "mac", "version": "1.1.6.9000", "date": "2026-10-03T10:21:28.000Z", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/8d22dfd30da1fb03f7d84720cacf9ee143c4c7fd7ca916baa1d77d16a2c3c0e0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.6.9000", "date": "2026-10-03T10:20:08.000Z", "arch": "emscripten", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/5e6f9c27d2de516d7e35dae5fb584d4d65edc9fe37f264fed86cdcf5f729da05", "status": "success", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.7.0", "os": "win", "version": "1.1.6.9000", "date": "2026-10-03T10:23:47.000Z", "arch": "aarch64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/71fbd5806cd28dfdc26481695070a00a927c51b4ed266c61dfa32dd1d4e0b2d0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.7.0", "os": "win", "version": "1.1.6.9000", "date": "2026-10-03T10:19:34.000Z", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/30355d876b8a2cc9eeda9f7afda340c22bfa1f7049654cf863c506ce618ed5e8", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.5.3", "os": "win", "version": "1.1.6.9000", "date": "2026-10-03T10:19:35.000Z", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/cf7f06e3158128fe8636de11fcf320f6396560069317d0103359574ab0bd7bbf", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.6.1", "os": "win", "version": "1.1.6.9000", "date": "2026-10-03T10:23:02.000Z", "arch": "aarch64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/8a30f2dc0ea2a0fb8a39e71934e52a28b71169804b855e0545405f0af38b56ca", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" }, { "r": "4.6.1", "os": "win", "version": "1.1.6.9000", "date": "2026-10-03T10:19:22.000Z", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/1062d11a38b8cbf28a6a98135c429c9395186f377c23b9ec4fa2c5b13882a992", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/37115759922" } ] }