{ "_id": "6a23db16530b9bc726be660a", "Package": "pgenlibr", "Type": "Package", "Title": "'PLINK' 2 Binary (.pgen) Reader", "Version": "0.6.2", "Date": "2026-06-05", "Authors@R": "c(person(given = \"Christopher\",\nfamily = \"Chang\",\nrole = c(\"aut\", \"cre\"),\nemail = \"chrchang@alumni.caltech.edu\"),\nperson(given = \"Eric\",\nfamily = \"Biggers\",\nrole = c(\"ctb\", \"cph\"),\ncomment = \"Author of included libdeflate library\"),\nperson(given = \"Yann\",\nfamily = \"Collet\",\nrole = c(\"ctb\"),\ncomment = \"Author of included Zstd library\"),\nperson(given = \"Meta Platforms, Inc.\",\nrole = c(\"cph\"),\ncomment = \"Zstd library\"),\nperson(given = \"Evan\",\nfamily = \"Nemerson\",\nrole = c(\"ctb\", \"cph\"),\ncomment = \"Author of included SIMDe library\"),\nperson(given = \"Przemyslaw\",\nfamily = \"Skibinski\",\nrole = c(\"ctb\"),\ncomment = \"Author of included Zstd library\"),\nperson(given = \"Nick\",\nfamily = \"Terrell\",\nrole = c(\"ctb\"),\ncomment = \"Author of included Zstd library\"))", "Description": "A thin wrapper over 'PLINK' 2's core libraries which\nprovides an R interface for reading .pgen files. A minimal\n.pvar loader is also included. Chang et al. (2015)\n.", "Encoding": "UTF-8", "License": "LGPL (>= 3)", "Copyright": "This package includes sources of the libdeflate library\nowned by Eric Biggers, sources of the SIMDe library owned by\nEvan Nemerson, sources of the Zstd library owned by Meta\nPlatforms, Inc., and sources of the pgenlib library owned by\nChristopher Chang.", "BugReports": "https://github.com/chrchang/plink-ng/issues", "RoxygenNote": "7.3.2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-06 08:26:18 UTC", "User": "root" }, "Author": "Christopher Chang [aut, cre], Eric Biggers [ctb, cph] (Author\nof included libdeflate library), Yann Collet [ctb] (Author of\nincluded Zstd library), Meta Platforms, Inc. [cph] (Zstd\nlibrary), Evan Nemerson [ctb, cph] (Author of included SIMDe\nlibrary), Przemyslaw Skibinski [ctb] (Author of included Zstd\nlibrary), Nick Terrell [ctb] (Author of included Zstd library)", "Maintainer": "Christopher Chang ", "Repository": "https://chrchang.r-universe.dev", "Date/Publication": "2026-06-06 02:30:02 UTC", "RemoteUrl": "https://github.com/cran/pgenlibr", "RemoteRef": "HEAD", "RemoteSha": "61d513f8dbc7d5f86487a2280cd3f71c8d67f273", "MD5sum": "8bed6bc8c0056413ea5352b742498e56", "_user": "chrchang", "_type": "src", "_file": "pgenlibr_0.6.2.tar.gz", "_fileid": "049b4ae07c9d5940ab425a09e1c82b2954afc0d26026939cbe4bfc5857984a68", "_filesize": 1611584, "_sha256": "049b4ae07c9d5940ab425a09e1c82b2954afc0d26026939cbe4bfc5857984a68", "_created": "2026-06-06T08:26:18.000Z", "_published": "2026-06-06T08:32:22.488Z", "_distro": "noble", "_jobs": [ { "job": 79864213464, "time": 141, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7452849892" }, { 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resources.", "topics": [ "ClosePgen" ] }, { "page": "ClosePvar", "title": "Closes a pvar object, releasing memory.", "topics": [ "ClosePvar" ] }, { "page": "GetAlleleCode", "title": "Look up an allele code.", "topics": [ "GetAlleleCode" ] }, { "page": "GetAlleleCt", "title": "Returns the effective number of alleles for a variant. Note that if no pvar was provided to the NewPgen() call, this function may return 2 even at multiallelic variants, since the .pgen may not store allele-count information.", "topics": [ "GetAlleleCt" ] }, { "page": "GetMaxAlleleCt", "title": "Returns the maximum GetAlleleCt() value across all variants in the file.", "topics": [ "GetMaxAlleleCt" ] }, { "page": "GetRawSampleCt", "title": "Returns the number of samples in the file.", "topics": [ "GetRawSampleCt" ] }, { "page": "GetVariantChrom", "title": "Retrieve chromosome ID for given variant index.", "topics": [ "GetVariantChrom" ] }, { "page": "GetVariantCt", "title": "Returns the number of variants in the file.", "topics": [ "GetVariantCt" ] }, { "page": "GetVariantId", "title": "Convert variant index to variant ID string.", "topics": [ "GetVariantId" ] }, { "page": "GetVariantPos", "title": "Retrieve POS (base-pair coordinate on a chromosome) for given variant index.", "topics": [ "GetVariantPos" ] }, { "page": "GetVariantsById", "title": "Convert variant ID string to variant index(es).", "topics": [ "GetVariantsById" ] }, { "page": "HardcallPhasePresent", "title": "Returns whether explicitly phased hardcalls are present.", "topics": [ "HardcallPhasePresent" ] }, { "page": "HasSparse", "title": "Returns whether dosages for the variant_numth variant and given allele are represented in a sparse manner that is supported by ReadSparse(), under the current sample subset.", "topics": [ "HasSparse" ] }, { "page": "HasSparseHardcalls", "title": "Returns whether hardcalls for the variant_numth variant and given allele are represented in a sparse manner that is supported by ReadSparseHardcalls().", "topics": [ "HasSparseHardcalls" ] }, { "page": "IntAlleleCodeBuf", "title": "Returns an empty two-row integer matrix that ReadAlleles() can load to.", "topics": [ "IntAlleleCodeBuf" ] }, { "page": "IntBuf", "title": "Returns an integer buffer that ReadHardcalls() can load to.", "topics": [ "IntBuf" ] }, { "page": "NewPgen", "title": "Opens a .pgen or PLINK 1 .bed file.", "topics": [ "NewPgen" ] }, { "page": "NewPvar", "title": "Loads variant positions, IDs, and allele codes from a .pvar or .bim file (which can be compressed with gzip or Zstd).", "topics": [ "NewPvar" ] }, { "page": "Read", "title": "Loads the variant_numth variant, and then fills buf with numeric dosages in [0, 2] indicating the dosages of the first ALT (or user-specified) allele for each sample, with missing values represented by NA.", "topics": [ "Read" ] }, { "page": "ReadAlleles", "title": "Loads the variant_numth variant, and then fills acbuf with integer allele codes, where each column of the buffer corresponds to a sample. 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