{ "_id": "6a1d623a1d7bb097a0a4aa6d", "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": "2026-06-01 10:27:55 UTC", "User": "root" }, "Author": "Alejandro Ochoa [aut, cre] (ORCID:\n)", "Maintainer": "Alejandro Ochoa ", "MD5sum": "76f92ef3bd81c445e960ee7639f216a0", "_user": "ochoalab", "_type": "src", "_file": "genio_1.1.6.9000.tar.gz", "_fileid": "4bd0e7edd19eeadccb58ed5b82b3452961135e043d1f8e41d057a2e3407e1aee", "_filesize": 782595, "_sha256": "4bd0e7edd19eeadccb58ed5b82b3452961135e043d1f8e41d057a2e3407e1aee", "_created": "2026-06-01T10:27:55.000Z", "_published": "2026-06-01T10:43:06.392Z", "_distro": "noble", "_jobs": [ { "job": 78833180134, "time": 139, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7329168964" }, { "job": 78833180226, "time": 139, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7329168420" }, { "job": 78833180505, "time": 142, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7329169830" }, { "job": 78833180144, "time": 175, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7329323466" }, { "job": 78833180265, "time": 387, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "7329363512" }, { "job": 78833180124, "time": 138, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7329395173" }, { "job": 78833180181, "time": 286, "config": "macos-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7329345847" }, { "job": 78832595458, "time": 232, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7329124329" }, { "job": 78833180034, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7329165652" }, { "job": 78833180081, "time": 139, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7329169846" }, { "job": 78833180103, "time": 115, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7329161146" }, { "job": 78833180096, "time": 117, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7329162113" } ], "_buildurl": "https://github.com/r-universe/ochoalab/actions/runs/26749202820", "_status": "success", "_host": "GitHub-Actions", "_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 }, "_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": 18, "_contributors": [ { "user": "alexviiia", "count": 104, "uuid": 12603341 } ], "_userbio": { "uuid": 41968176, "type": "organization", "name": "Ochoa Lab at Duke StatGen", "description": "Research in statgen, biostats, compbio" }, "_downloads": { "count": 1261, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/genio" }, "_devurl": "https://github.com/ochoalab/genio", "_searchresults": 412, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_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", 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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": 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