{ "_id": "6a1ad0151d7bb097a09e1193", "Package": "GBScleanR", "Type": "Package", "Title": "Error correction tool for noisy genotyping by sequencing (GBS)\ndata", "Version": "2.7.0", "Date": "2026-03-31", "Authors@R": "person(\"Tomoyuki\", \"Furuta\", \nemail = \"f.tomoyuki@okayama-u.ac.jp\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0869-6626\"))", "Description": "GBScleanR is a package for quality check, filtering, and\nerror correction of genotype data derived from next generation\nsequcener (NGS) based genotyping platforms. GBScleanR takes\nVariant Call Format (VCF) file as input. The main function of\nthis package is `estGeno()` which estimates the true genotypes\nof samples from given read counts for genotype markers using a\nhidden Markov model with incorporating uneven observation ratio\nof allelic reads. This implementation gives robust genotype\nestimation even in noisy genotype data usually observed in\nGenotyping-By-Sequnencing (GBS) and similar methods, e.g.\nRADseq. The current implementation accepts genotype data of a\ndiploid population at any generation of multi-parental cross,\ne.g. biparental F2 from inbred parents, biparental F2 from\noutbred parents, and 8-way recombinant inbred lines (8-way\nRILs) which can be refered to as MAGIC population.", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "SystemRequirements": "GNU make, C++11", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "biocViews": "GeneticVariability, SNP, Genetics, HiddenMarkovModel,\nSequencing, QualityControl", "BugReports": "https://github.com/tomoyukif/GBScleanR/issues", "URL": "https://github.com/tomoyukif/GBScleanR", "Config/testthat/edition": "3", "Config/pak/sysreqs": "make libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:57:36 UTC", "RemoteUrl": "https://github.com/bioc/GBScleanR", "RemoteRef": "HEAD", "RemoteSha": "5d24eee2369b1f4578700fb93a770cd5ca0b478a", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 08:18:09 UTC", "User": "root" }, "Author": "Tomoyuki Furuta [aut, cre] (ORCID:\n)", "Maintainer": "Tomoyuki Furuta ", "MD5sum": "ed04a55d6dbc6a1829df45e033b021a9", "_user": "bioc", "_type": "src", "_file": "GBScleanR_2.7.0.tar.gz", "_fileid": "b4d360355e40ed939818d4006578a2fdbfcb6ce7fdb8e983fa5241159d79a8aa", "_filesize": 2110946, "_sha256": "b4d360355e40ed939818d4006578a2fdbfcb6ce7fdb8e983fa5241159d79a8aa", "_created": "2026-05-30T08:18:09.000Z", "_published": "2026-05-30T11:55:01.288Z", "_jobs": [ { "job": 78636103968, "time": 192, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306791110" }, { "job": 78636104000, "time": 268, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7306798696" }, { "job": 78636103987, "time": 340, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306805788" }, { "job": 78636104005, "time": 262, "config": 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"windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306799623" }, { "job": 78636104009, "time": 277, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306799619" }, { "job": 78636104026, "time": 279, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306799981" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678965665", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/GBScleanR", "_commit": { "id": "5d24eee2369b1f4578700fb93a770cd5ca0b478a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381056 }, "_maintainer": { "name": "Tomoyuki Furuta", "email": "f.tomoyuki@okayama-u.ac.jp", "login": "tomoyukif", "orcid": "0000-0002-0869-6626", "description": "", "uuid": 40555133 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "SeqArray", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppParallel", "role": "LinkingTo" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "expm", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "RcppParallel", "role": "Imports" }, { "package": "gdsfmt", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-25", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2025-46", "n": 2 }, { "week": "2025-47", "n": 1 }, { "week": "2025-48", "n": 1 }, { "week": 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"extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GBScleanR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/tomoyukif/gbscleanr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "addScheme", "assignScheme", "boxplotGBSR", "closeGDS", "countGenotype", "countRead", "estGeno", "gbsrGDS2CSV", "gbsrGDS2VCF", "gbsrVCF2GDS", "getAllele", "getChromosome", "getCountAlleleAlt", "getCountAlleleMissing", "getCountAlleleRef", "getCountGenoAlt", "getCountGenoHet", "getCountGenoMissing", "getCountGenoRef", "getCountRead", "getCountReadAlt", "getCountReadRef", "getFixedParameter", "getGenotype", "getHaplotype", "getInfo", "getMAC", "getMAF", "getMarID", "getMeanReadAlt", "getMeanReadRef", "getMedianReadAlt", "getMedianReadRef", "getParents", "getPloidy", "getPosition", "getRead", "getReplicates", "getSamID", "getSDReadAlt", "getSDReadRef", "histGBSR", "initScheme", "isOpenGDS", "loadGDS", 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"title": "Count genotype calls and alleles per sample and per marker.", "topics": [ "countGenotype", "countGenotype,GbsrGenotypeData-method" ] }, { "page": "countRead", "title": "Count reads per sample and per marker.", "topics": [ "countRead", "countRead,GbsrGenotypeData-method" ] }, { "page": "estGeno", "title": "Genotype estimation using a hiden Morkov model", "topics": [ "estGeno", "estGeno,GbsrGenotypeData-method" ] }, { "page": "gbsrGDS2CSV", "title": "Write a CSV file based on data in a GDS file", "topics": [ "gbsrGDS2CSV", "gbsrGDS2CSV,GbsrGenotypeData-method" ] }, { "page": "gbsrGDS2VCF", "title": "Write a VCF file based on data in a GDS file", "topics": [ "gbsrGDS2VCF", "gbsrGDS2VCF,GbsrGenotypeData-method" ] }, { "page": "GbsrGenotypeData-class", "title": "Class GbsrGenotypeData", "topics": [ "GbsrGenotypeData", "GbsrGenotypeData-class" ] }, { "page": "GbsrScheme-class", "title": "Class 'GbsrScheme'", "topics": [ "GbsrScheme", "GbsrScheme-class" ] }, { "page": "gbsrVCF2GDS", "title": "Convert a VCF file to a GDS file", "topics": [ "gbsrVCF2GDS" ] }, { "page": "getAllele", "title": "Obtain reference allele information of markers", "topics": [ "getAllele", "getAllele,GbsrGenotypeData-method" ] }, { "page": "getChromosome", "title": "Obtain chromosome IDs of markers", "topics": [ "getChromosome", "getChromosome,GbsrGenotypeData-method" ] }, { "page": "getCountAlleleAlt", "title": "Obtain total alternative allele counts per SNP or per sample", "topics": [ "getCountAlleleAlt", "getCountAlleleAlt,GbsrGenotypeData-method" ] }, { "page": "getCountAlleleMissing", "title": "Obtain total missing allele counts per SNP or per sample", "topics": [ "getCountAlleleMissing", "getCountAlleleMissing,GbsrGenotypeData-method" ] }, { "page": "getCountAlleleRef", "title": "Obtain total reference allele counts per SNP or per sample", "topics": [ "getCountAlleleRef", "getCountAlleleRef,GbsrGenotypeData-method" ] }, { "page": "getCountGenoAlt", "title": "Obtain total alternative genotype counts per SNP or per sample", "topics": [ "getCountGenoAlt", "getCountGenoAlt,GbsrGenotypeData-method" ] }, { "page": "getCountGenoHet", "title": "Obtain total heterozygote counts per SNP or per sample", "topics": [ "getCountGenoHet", "getCountGenoHet,GbsrGenotypeData-method" ] }, { "page": "getCountGenoMissing", "title": "Obtain total missing genotype counts per SNP or per sample", "topics": [ "getCountGenoMissing", "getCountGenoMissing,GbsrGenotypeData-method" ] }, { "page": "getCountGenoRef", "title": "Obtain total reference genotype counts per SNP or per sample", "topics": [ "getCountGenoRef", "getCountGenoRef,GbsrGenotypeData-method" ] }, { "page": "getCountRead", "title": "Obtain total read counts per SNP or per sample", "topics": [ "getCountRead", "getCountRead,GbsrGenotypeData-method" ] }, { "page": "getCountReadAlt", "title": "Obtain total alternative read counts per SNP or per sample", "topics": [ "getCountReadAlt", "getCountReadAlt,GbsrGenotypeData-method" ] }, { "page": "getCountReadRef", "title": "Obtain total reference read counts per SNP or per sample", "topics": [ "getCountReadRef", "getCountReadRef,GbsrGenotypeData-method" ] }, { "page": "getFixedParameter", "title": "Get fixed allele read biases and mismapping rate", "topics": [ "getFixedParameter", "getFixedParameter,GbsrGenotypeData-method" ] }, { "page": "getGenotype", "title": "Get genotype call data.", "topics": [ "getGenotype", "getGenotype,GbsrGenotypeData-method" ] }, { "page": "getHaplotype", "title": "Get haplotype call data.", "topics": [ "getHaplotype", "getHaplotype,GbsrGenotypeData-method" ] }, { "page": "getInfo", "title": "Obtain information stored in the \"annotation/info\" node", "topics": [ "getInfo", "getInfo,GbsrGenotypeData-method" ] }, { "page": "getMAC", "title": "Obtain minor allele counts per SNP or per sample", "topics": [ "getMAC", "getMAC,GbsrGenotypeData-method" ] }, { "page": "getMAF", "title": "Obtain minor allele frequencies per SNP or per sample", "topics": [ "getMAF", "getMAF,GbsrGenotypeData-method" ] }, { "page": "getMarID", "title": "Obtain the marker IDs", "topics": [ "getMarID", "getMarID,GbsrGenotypeData-method" ] }, { "page": "getMeanReadAlt", "title": "Obtain mean values of total alternative read counts per SNP or per sample", "topics": [ "getMeanReadAlt", "getMeanReadAlt,GbsrGenotypeData-method" ] }, { "page": "getMeanReadRef", "title": "Obtain mean values of total reference read counts per SNP or per sample", "topics": [ "getMeanReadRef", "getMeanReadRef,GbsrGenotypeData-method" ] }, { "page": "getMedianReadAlt", "title": "Obtain quantile values of total alternative read counts per SNP or per sample", "topics": [ "getMedianReadAlt", "getMedianReadAlt,GbsrGenotypeData-method" ] }, { "page": "getMedianReadRef", "title": "Obtain quantile values of total reference read counts per SNP or per sample", "topics": [ "getMedianReadRef", "getMedianReadRef,GbsrGenotypeData-method" ] }, { "page": "getParents", "title": "Get parental sample information", "topics": [ "getParents", "getParents,GbsrGenotypeData-method" ] }, { "page": "getPloidy", "title": "Get ploidy", "topics": [ "getPloidy", "getPloidy,GbsrGenotypeData-method" ] }, { "page": "getPosition", "title": "Obtain marker positions", "topics": [ "getPosition", "getPosition,GbsrGenotypeData-method" ] }, { "page": "getRead", "title": "Get read count data.", "topics": [ "getRead", "getRead,GbsrGenotypeData-method" ] }, { "page": "getReplicates", "title": "Get identifiers to indicates which samples are replicates.", "topics": [ "getReplicates", "getReplicates,GbsrGenotypeData-method" ] }, { "page": "getSamID", "title": "Obtain the sample IDs", "topics": [ "getSamID", "getSamID,GbsrGenotypeData-method" ] }, { "page": "getSDReadAlt", "title": "Obtain standard deviations of total alternative read counts per SNP or per sample", "topics": [ "getSDReadAlt", "getSDReadAlt,GbsrGenotypeData-method" ] }, { "page": "getSDReadRef", "title": "Obtain standard deviations of total reference read counts per SNP or per sample", "topics": [ "getSDReadRef", "getSDReadRef,GbsrGenotypeData-method" ] }, { "page": "histGBSR", "title": "Draw histograms of specified statistics", "topics": [ "histGBSR" ] }, { "page": "initScheme", "title": "Build a GbsrScheme object", "topics": [ "initScheme", "initScheme,GbsrGenotypeData-method", "initScheme,GbsrScheme-method" ] }, { "page": "isOpenGDS", "title": "Check if a GDS file has been opened or not.", "topics": [ "isOpenGDS", "isOpenGDS,GbsrGenotypeData-method" ] }, { "page": "loadGDS", "title": "Load a GDS file and construct a GbsrGenotypeData object.", "topics": [ "loadGDS" ] }, { "page": "makeScheme", "title": "Automate a GbsrScheme object building.", "topics": [ "makeScheme", "makeScheme,GbsrGenotypeData-method" ] }, { "page": "nmar", "title": "Return the number of SNPs.", "topics": [ "nmar", "nmar,GbsrGenotypeData-method" ] }, { "page": "nsam", "title": "Return the number of samples.", "topics": [ "nsam", "nsam,GbsrGenotypeData-method" ] }, { "page": "pairsGBSR", "title": "Draw a scatter plot of a pair of specified statistics", "topics": [ "pairsGBSR" ] }, { "page": "plotDosage", "title": "Draw line plots of allele dosage per marker per sample.", "topics": [ "plotDosage" ] }, { "page": "plotGBSR", "title": "Draw line plots of specified statistics", "topics": [ "plotGBSR" ] }, { "page": "plotReadRatio", "title": "Draw line plots of proportion of reference allele read counts per marker per sample.", "topics": [ "plotReadRatio" ] }, { "page": "reopenGDS", "title": "Reopen the connection to the GDS file.", "topics": [ "reopenGDS", "reopenGDS,GbsrGenotypeData-method" ] }, { "page": "resetCallFilter", "title": "Set the origina; data to be used in GBScleanR's functions", "topics": [ "resetCallFilter", "resetCallFilter,GbsrGenotypeData-method" ] }, { "page": "resetFilter", "title": "Reset all filters made by 'setSamFilter()', 'setMarFilter()', and 'setCallFilter()'.", "topics": [ "resetFilter", "resetFilter,GbsrGenotypeData-method" ] }, { "page": "resetMarFilter", "title": "Reset the filter made by 'setMarFilter()'", "topics": [ "resetMarFilter", "resetMarFilter,GbsrGenotypeData-method" ] }, { "page": "resetSamFilter", "title": "Reset the filter made by 'setSamFilter()'", "topics": [ "resetSamFilter", "resetSamFilter,GbsrGenotypeData-method" ] }, { "page": "setCallFilter", "title": "Filter out each genotype call meeting criteria", "topics": [ "setCallFilter", "setCallFilter,GbsrGenotypeData-method" ] }, { "page": "setFixedParameter", "title": "Set fixed allele read biases and mismapping rate", "topics": [ "setFixedParameter", "setFixedParameter,GbsrGenotypeData-method" ] }, { "page": "setInfoFilter", "title": "Filter out markers based on marker quality metrics", "topics": [ "setInfoFilter", "setInfoFilter,GbsrGenotypeData-method" ] }, { "page": "setMarFilter", "title": "Filter out markers", "topics": [ "setMarFilter", "setMarFilter,GbsrGenotypeData-method" ] }, { "page": "setParents", "title": "Set labels to samples which should be recognized as parents of the population to be subjected to error correction.", "topics": [ "setParents", "setParents,GbsrGenotypeData-method" ] }, { "page": "setPloidy", "title": "Set ploidy", "topics": [ "setPloidy", "setPloidy,GbsrGenotypeData-method" ] }, { "page": "setReplicates", "title": "Set identifiers to indicates which samples are replicates.", "topics": [ "setReplicates", "setReplicates,GbsrGenotypeData-method" ] }, { "page": "setSamFilter", "title": "Filter out samples", "topics": [ "setSamFilter", "setSamFilter,GbsrGenotypeData-method" ] }, { "page": "showScheme", "title": "Show the information stored in a GbsrScheme object", "topics": [ "showScheme", "showScheme,GbsrGenotypeData-method", "showScheme,GbsrScheme-method" ] }, { "page": "thinMarker", "title": "Remove markers potentially having redundant information.", "topics": [ "thinMarker", "thinMarker,GbsrGenotypeData-method" ] }, { "page": "validMar", "title": 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