{ "_id": "6a632eeed3420cf5dfdb848b", "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": "2026-07-24 07:34:00 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/8e913bcfbbe2ad4531876925deee6da3ea3186edd97e0d11ea1d17434ac73944", "_filesize": 781245, "_sha256": "8e913bcfbbe2ad4531876925deee6da3ea3186edd97e0d11ea1d17434ac73944", "_expires": "2026-11-01T09:22:52.000Z", "_created": "2026-07-24T07:34:00.000Z", "_published": "2026-07-24T09:22:54.534Z", "_jobs": [ { "job": 89426480179, "time": 128, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8589870417" }, { "job": 89426480180, "time": 145, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8589876843" }, { "job": 89426480163, "time": 118, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8589867212" }, { "job": 89426480175, "time": 150, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8589879227" }, { "job": 89426480242, "time": 194, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "8592250327" }, { "job": 89426480226, "time": 230, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "8592299165" }, { "job": 89426480171, "time": 136, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "8592202452" }, { "job": 89426480169, "time": 205, "config": "macos-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8592177924" }, { "job": 89425907934, "time": 197, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8589824382" }, { "job": 89426480120, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8589869237" }, { "job": 89426480133, "time": 116, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8589866166" }, { "job": 89426480167, "time": 124, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "8589869476" }, { "job": 89426480230, "time": 112, "config": "windows-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8589865426" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200", "_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": 6, "description": "Research in statgen, biostats, compbio" }, "_downloads": { "count": 953, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/genio" }, "_devurl": "https://github.com/ochoalab/genio", "_searchresults": 447, "_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/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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": 7.88330363352409, "_indexed": true, "_nocasepkg": "genio", "_universes": [ "ochoalab", "alexviiia" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.6.9000", "date": "2026-07-24T07:36:11.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/0347e736363e67fa3037907577ef321ee0ddb14a77275282ee3037e44886eed4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.7.0", "os": "linux", "version": "1.1.6.9000", "date": "2026-07-24T07:36:24.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/71ce721271247efc1c5b2e874d2a7ffda3f6fa8745b54c45f6dedc14cf49360c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.6.1", "os": "linux", "version": "1.1.6.9000", "date": "2026-07-24T07:36:04.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/84fcf989813aac73cf612ee6ab6f0f96b112b9724ec5ff8adf3b453e4dc1eca9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.6.1", "os": "linux", "version": "1.1.6.9000", "date": "2026-07-24T07:36:29.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/d52d698be0fdf86beec32ffe6cf8b56d8765accf294aa891ef77cf51a3b1cc64", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.5.3", "os": "mac", "version": "1.1.6.9000", "date": "2026-07-24T09:19:50.000Z", "arch": "aarch64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/8acf0b98fc8477bd145f97c40db4b7d68036d9a343ca2e3f9c9d0f31b1fa8240", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.5.3", "os": "mac", "version": "1.1.6.9000", "date": "2026-07-24T09:21:48.000Z", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/a73ba4f9b98708bfd0150ec45a67178e55da03852be6d3463c32f8280dcb99dc", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.6.1", "os": "mac", "version": "1.1.6.9000", "date": "2026-07-24T09:17:48.000Z", "arch": "aarch64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/b68236fc2ff2d7963fc33129c0804b59c4cf15f1539637f3c88af65dc310c35b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.6.1", "os": "mac", "version": "1.1.6.9000", "date": "2026-07-24T09:16:40.000Z", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/ee057208aa383b02e6a80a80325ad6242925669f53f7d8894ae47edf3278f6dd", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.6.9000", "date": "2026-07-24T07:36:19.000Z", "arch": "emscripten", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/ac1749f143a2fdc8102acae869e296ca91408e5d0d307d99e5da6a0b42a5cd49", "status": "success", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.7.0", "os": "win", "version": "1.1.6.9000", "date": "2026-07-24T07:35:21.000Z", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/882bc7fe780a5a626daa6a7dfb8721cf6d881d445135089c77b94df0fe150c17", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.5.3", "os": "win", "version": "1.1.6.9000", "date": "2026-07-24T07:35:31.000Z", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/ab78f683fca5ddf9b00d58332719377d96d5e305d3e4b926779fd9b09cc1241f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" }, { "r": "4.6.1", "os": "win", "version": "1.1.6.9000", "date": "2026-07-24T07:35:21.000Z", "arch": "x86_64", "commit": "b776208acca322e3d858c2785e81f0af4f0d0b6d", "fileid": "https://r2.ropensci.org/ac4a5ffe237d72c11731e21852b975395572c21a081cc661ef2627e54067ec8b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ochoalab/actions/runs/30075707200" } ] }