{ "_id": "6a10a29eacfb0bcc41cb9e5c", "Package": "qtl2fst", "Version": "0.30", "Date": "2024-11-23", "Title": "Database Storage of Genotype Probabilities for QTL Mapping", "Description": "Uses the 'fst' package to store genotype probabilities on\ndisk for the 'qtl2' package. These genotype probabilities are a\ncentral data object for mapping quantitative trait loci (QTL),\nbut they can be quite large. The facilities in this package\nenable the genotype probabilities to be stored on disk, leading\nto reduced memory usage with only a modest increase in\ncomputation time.", "Author": "Karl W Broman [aut, cre]\n(), Brian S Yandell\n[aut] (), Petr Simecek\n[aut] ()", "Maintainer": "Karl W Broman ", "Authors@R": "c(person(\"Karl W\", \"Broman\", role=c(\"aut\", \"cre\"),\nemail=\"broman@wisc.edu\", comment=c(ORCID = \"0000-0002-4914-6671\")),\nperson(\"Brian S\", \"Yandell\", role=\"aut\",\nemail=\"byandell@wisc.edu\", comment=c(ORCID = \"0000-0002-8774-9377\")),\nperson(\"Petr\", \"Simecek\", role=\"aut\", comment=c(ORCID = \"0000-0002-2922-7183\")))", "VignetteBuilder": "knitr", "License": "GPL-3", "URL": "https://github.com/rqtl/qtl2fst", "ByteCompile": "true", "Encoding": "UTF-8", "Roxygen": "list(markdown=TRUE)", "Config/roxygen2/version": "8.0.0", "Repository": "https://rqtl.r-universe.dev", "Date/Publication": "2026-05-22 11:32:12 UTC", "RemoteUrl": "https://github.com/rqtl/qtl2fst", "RemoteRef": "HEAD", "RemoteSha": "b7de82f7404c7347904ab91c01160df822baa686", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 18:34:30 UTC", "User": "root" }, "MD5sum": "505bd48e9f151388300c23ae9471672d", "_user": "rqtl", "_type": "src", "_file": "qtl2fst_0.30.tar.gz", "_fileid": "e447bd044029e6997974c29201c55daa32a10d3b201d519077d32a3aab9fc6bc", "_filesize": 159921, "_sha256": "e447bd044029e6997974c29201c55daa32a10d3b201d519077d32a3aab9fc6bc", "_created": "2026-05-22T18:34:30.000Z", "_published": "2026-05-22T18:38:22.958Z", "_distro": "noble", "_jobs": [ { "job": 77440644268, "time": 178, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7167809196" }, { "job": 77440644253, "time": 128, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7167793846" }, { "job": 77440644277, "time": 182, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7167803877" }, { "job": 77440644242, "time": 187, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7167800366" }, { "job": 77440177155, "time": 183, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7167755725" }, { "job": 77440644237, "time": 109, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7167788560" }, { "job": 77440644246, "time": 199, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7167815659" }, { "job": 77440644288, "time": 100, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7167785916" }, { "job": 77440644287, "time": 107, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7167788075" } ], "_buildurl": "https://github.com/r-universe/rqtl/actions/runs/26291330877", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rqtl/qtl2fst", "_commit": { "id": "b7de82f7404c7347904ab91c01160df822baa686", "author": "Karl Broman ", "committer": "Karl Broman ", "message": "README: Add more installation instructions (r universe; github)\n", "time": 1779449532 }, "_maintainer": { "name": "Karl W Broman", "email": "broman@wisc.edu", "login": "kbroman", "mastodon": "@kbroman@rstats.me", "orcid": "0000-0002-4914-6671", "description": "Professor in Dept of Biostatistics & Medical Informatics at UW–Madison. Applied statistician working on statistical genomics.\n", "uuid": 53972 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.0", "role": "Depends" }, { "package": "fst", "role": "Imports" }, { "package": "qtl2", "version": ">= 0.24", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "rqtl", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2026-21", "n": 3 } ], "_tags": [], "_stars": 2, "_contributors": [ { "user": "kbroman", "count": 110, "uuid": 53972 } ], "_userbio": { "uuid": 9142954, "type": "organization", "name": "R/qtl" }, "_downloads": { "count": 270, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/qtl2fst" }, "_devurl": "https://github.com/rqtl/qtl2fst", "_searchresults": 17, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/qtl2fst.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/rqtl/qtl2fst", "_realowner": "rqtl", "_cranurl": true, "_releases": [ { "version": "0.22-7", "date": "2020-07-30" }, { "version": "0.24", "date": "2021-04-29" }, { "version": "0.26", "date": "2021-10-07" }, { "version": "0.28", "date": "2024-07-16" }, { "version": "0.30", "date": "2024-11-23" } ], "_exports": [ "calc_genoprob_fst", "cbind.fst_genoprob", "fst_extract", "fst_files", "fst_genoprob", "fst_genoprob_restore", "fst_path", "fst_restore", "fst2calc_genoprob", "genoprob_to_alleleprob_fst", "rbind.fst_genoprob", "replace_path", "subset_fst_genoprob" ], "_help": [ { "page": "calc_genoprob_fst", "title": "Calculate conditional genotype probabilities and write to fst database", "topics": [ "calc_genoprob_fst" ] }, { "page": "cbind.fst_genoprob", "title": "Join genotype probabilities for different chromosomes", "topics": [ "cbind.fst_genoprob" ] }, { "page": "fst_extract", "title": "Extract genotype probabilities from fst database", "topics": [ "fst2calc_genoprob", "fst_extract" ] }, { "page": "fst_files", "title": "List files used in fst_genoprob object", "topics": [ "fst_files" ] }, { "page": "probs2fst", "title": "Store genotype probabilities in fst database", "topics": [ "fst_genoprob" ] }, { "page": "fst_path", "title": "Path used in fst_genoprob object", "topics": [ "fst_path" ] }, { "page": "fst_restore", "title": "Restore fst_genoprob object to original dimensions.", "topics": [ "fst_genoprob_restore", "fst_restore" ] }, { "page": "genoprob_to_alleleprob_fst", "title": "Convert genotype probabilities to allele probabilities and write to fst database", "topics": [ "genoprob_to_alleleprob_fst" ] }, { "page": "rbind.fst_genoprob", "title": "Join genotype probabilities for different individuals", "topics": [ "rbind.fst_genoprob" ] }, { "page": "replace_path", "title": "Replace the path used in fst_genoprob object", "topics": [ "replace_path" ] }, { "page": "subset_fst_genoprob", "title": "Subsetting genotype probabilities", "topics": [ "subset.fst_genoprob", "subset_fst_genoprob" ] }, { "page": "summary.fst_genoprob", "title": "Summary of an fst_genoprob object", "topics": [ "summary.fst_genoprob" ] } ], "_readme": "https://github.com/rqtl/qtl2fst/raw/HEAD/README.md", "_rundeps": [ "bit", "bit64", "blob", "cachem", "cli", "cpp11", "data.table", "DBI", "fastmap", "fst", "fstcore", "glue", "jsonlite", "lifecycle", "memoise", "pkgconfig", "qtl2", "Rcpp", "RcppEigen", "rlang", "RSQLite", "vctrs", "yaml" ], "_vignettes": [ { "source": "qtl2fst.Rmd", "filename": "qtl2fst.html", "title": "qtl2fst user guide", "engine": "knitr::rmarkdown", "headings": [ "Selecting one chromosome", "Subsetting by ind, chr, mar", "Binding by columns or rows", "Looking under the hood", "Paths", "Direct construction of the fst database", "Genome scans" ], "created": "2019-07-16 00:11:48", "modified": "2021-04-28 23:28:24", "commits": 6 } ], "_score": 4.707570176097937, "_indexed": true, "_nocasepkg": "qtl2fst", "_universes": [ "rqtl", "kbroman" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.30", "date": "2026-05-22T18:37:11.000Z", "distro": "noble", "commit": "b7de82f7404c7347904ab91c01160df822baa686", "fileid": "9657c6cefcfb251067e170e01503947d7bc18d22590c03ace03ca2d04e67c2b9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rqtl/actions/runs/26291330877" }, { "r": "4.6.0", "os": "linux", "version": "0.30", "date": "2026-05-22T18:36:23.000Z", "distro": "noble", "commit": "b7de82f7404c7347904ab91c01160df822baa686", "fileid": "e858b4cc21838711fdb932d77c6d6ab9b9474a9e58b7d28e393b1f37bf74397a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rqtl/actions/runs/26291330877" }, { "r": "4.5.3", "os": "mac", "version": "0.30", "date": "2026-05-22T18:37:03.000Z", "commit": "b7de82f7404c7347904ab91c01160df822baa686", "fileid": "9ef4e2a098afa4542a7cfe5b41de2bc8afec32e95c0b047fe1bf52de077583c1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rqtl/actions/runs/26291330877" }, { "r": "4.6.0", "os": "mac", "version": "0.30", "date": "2026-05-22T18:36:52.000Z", "commit": "b7de82f7404c7347904ab91c01160df822baa686", "fileid": "d32e5f18628942a4c4aca554bbfa4003c8bac5948a3da1f0a51f55ab8648e1ef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rqtl/actions/runs/26291330877" }, { "r": "4.6.0", "os": "wasm", "version": "0.30", "date": "2026-05-22T18:36:38.000Z", "commit": "b7de82f7404c7347904ab91c01160df822baa686", "fileid": "c99d2dad9ceade19cd7e3824a407dec71a2a30ec8a29431819664ecf54b2a95f", "status": "success", "buildurl": "https://github.com/r-universe/rqtl/actions/runs/26291330877" }, { "r": "4.7.0", "os": "win", "version": "0.30", "date": "2026-05-22T18:37:29.000Z", "commit": "b7de82f7404c7347904ab91c01160df822baa686", "fileid": "76076f5fa0dac50938ec3f1372fca9593f75d96463510f9fd3e9da182679989a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rqtl/actions/runs/26291330877" }, { "r": "4.5.3", "os": "win", "version": "0.30", "date": "2026-05-22T18:35:47.000Z", "commit": "b7de82f7404c7347904ab91c01160df822baa686", "fileid": "5c62ff9258f53ffb63b298cc6fa5b5fe4ecd5606e1c50b8889a1fe0c98ae2b80", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rqtl/actions/runs/26291330877" }, { "r": "4.6.0", "os": "win", "version": "0.30", "date": "2026-05-22T18:35:52.000Z", "commit": "b7de82f7404c7347904ab91c01160df822baa686", "fileid": "74c7108a0e9e363d5406c45ec8854bc2b105826e1c8d4ee7450577a0412f0a09", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rqtl/actions/runs/26291330877" } ] }