{ "_id": "6a0f7eaaacfb0bcc41c63bbf", "Package": "Qploidy", "Title": "Estimation of Ploidy and Detection of Aneuploidy Using\nGenotyping Data", "Version": "1.5.2", "Authors@R": "c(person(given='Cristiane', \nfamily='Taniguti',\nemail = 'cht47@cornell.edu',\nrole = c('cre', 'aut')),\nperson(given='Jeekin',\nfamily='Lau',\nemail = 'Jeekin.Lau@usda.gov',\nrole = c('ctb')),\nperson(given = \"Oscar\",\nfamily = \"Riera-Lizarazu\",\nrole = c(\"ctb\"))\n)", "Description": "Provides functions for estimating ploidy levels and\ndetecting aneuploidy in individuals using allele intensities or\nallele count data from high-throughput genotyping platforms,\nincluding single nucleotide polymorphism (SNP) arrays and\nsequencing-based technologies. Implements method described in\nTaniguti et al. (2025) an extended\nversion of the 'PennCNV' signal standardization method by Wang\net al. (2007) for higher ploidy\nlevels. Computes B-allele frequencies (BAF), z-scores, and\nidentifies copy number variation patterns.", "License": "AGPL (>= 3)", "biocViews": "", "Encoding": "UTF-8", "URL": "https://github.com/Cristianetaniguti/Qploidy", "BugReports": "https://github.com/Cristianetaniguti/Qploidy/issues", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "Language": "en-US", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://cristianetaniguti.r-universe.dev", "Date/Publication": "2026-05-21 20:30:56 UTC", "RemoteUrl": "https://github.com/cristianetaniguti/qploidy", "RemoteRef": "HEAD", "RemoteSha": "b2456f604b9bd54fcffa2d064d5b18135b24e0ce", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-21 21:47:02 UTC", "User": "root" }, "Author": "Cristiane Taniguti [cre, aut],\nJeekin Lau [ctb],\nOscar Riera-Lizarazu [ctb]", "Maintainer": "Cristiane Taniguti ", "MD5sum": "5c385f947871bd685cb44fdad0616516", "_user": "cristianetaniguti", "_type": "src", "_file": "Qploidy_1.5.2.tar.gz", "_fileid": "a2a46f99c0b88a28f0ace9ce912f0e4f438310ef248749face22c19e331febec", "_filesize": 4405542, "_sha256": "a2a46f99c0b88a28f0ace9ce912f0e4f438310ef248749face22c19e331febec", "_created": "2026-05-21T21:47:02.000Z", "_published": "2026-05-21T21:52:42.245Z", "_distro": "noble", "_jobs": [ { "job": 77275716767, "time": 241, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7148049880" }, { "job": 77275716733, "time": 239, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7148049700" }, { "job": 77275716765, "time": 205, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7148033023" }, { "job": 77275716768, "time": 188, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7148025983" }, { "job": 77274625835, "time": 431, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7147977481" }, { "job": 77275716749, "time": 141, "config": 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Coordinator, @Breeding-Insight \nUniversity of Florida/IFAS", "uuid": 7572527 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "vroom", "role": "Imports" }, { "package": "ggpubr", "role": "Imports" }, { "package": "multtest", "role": "Imports" }, { "package": "vcfR", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "updog", "role": "Suggests" }, { "package": "rmdformats", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.10", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cristianetaniguti", "_selfowned": true, 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"extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/cristianetaniguti/qploidy", "_realowner": "cristianetaniguti", "_cranurl": true, "_releases": [ { "version": "1.0.1", "date": "2025-05-01" } ], "_exports": [ "all_resolutions_plots", "area_estimate_ploidy", "clean_summary", "find_header_line", "get_aneuploids", "get_baf", "get_baf_par", "get_centers", "get_R_theta", "get_zscore", "merge_arms_format", "plot_baf", "plot_baf_hist", "plot_baf_with_ploidy_guides", "plot_qploidy_standardization", "plot_xy_with_ploidy_guides", "qploidy_read_vcf", "read_axiom", "read_illumina_array", "read_qploidy_standardization", "rm_outlier", "simulate_axiom_summary", "simulate_illumina_file", "simulate_standardization_input", "simulate_vcf", "standardize", "summary_to_fitpoly", "updog_centers", "vcf_sanity_check", "write_qploidy_standardization" ], "_help": [ { "page": "all_resolutions_plots", "title": "Plot graphics for ploidy visual inspection for each resolution", "topics": [ "all_resolutions_plots" ] }, { "page": "area_estimate_ploidy", "title": "Estimate ploidy using area method", "topics": [ "area_estimate_ploidy" ] }, { "page": "clean_summary", "title": "Clean Axiom Summary File", "topics": [ "clean_summary" ] }, { "page": "find_header_line", "title": "Find the Header Line in a File", "topics": [ "find_header_line" ] }, { "page": "get_aneuploids", "title": "indexes for aneuploids", "topics": [ "get_aneuploids" ] }, { "page": "get_baf", "title": "Calculate B-Allele Frequency (BAF) from Theta Values", "topics": [ "get_baf" ] }, { "page": "get_baf_par", "title": "To create baf in parallel", "topics": [ "get_baf_par" ] }, { "page": "get_centers", "title": "Estimate Cluster Centers for Genotype Dosage Classes", "topics": [ "get_centers" ] }, { "page": "get_R_theta", "title": "Get R and Theta Values from Summary File", "topics": [ "get_R_theta" ] }, { "page": "get_zscore", "title": "Calculate Z-Scores for Allele Intensities or Counts", "topics": [ "get_zscore" ] }, { "page": "is_compressed_file", "title": "Check if a File is Compressed", "topics": [ "is_compressed_file" ] }, { "page": "merge_arms_format", "title": "Merges chromosome-arm level analysis results into chromosome level format", "topics": [ "merge_arms_format" ] }, { "page": "mode", "title": "Calculate the Statistical Mode", "topics": [ "mode" ] }, { "page": "pascalTriangle", "title": "Pascal Triangle for Expected Peaks Calculation", "topics": [ "pascalTriangle" ] }, { "page": "plot_baf", "title": "Plot BAF", "topics": [ "plot_baf" ] }, { "page": "plot_baf_hist", "title": "Plot BAF Histogram", "topics": [ "plot_baf_hist" ] }, { "page": "plot_baf_with_ploidy_guides", "title": "Plot BAF-derived X–Y scatter with ploidy dosage guides (optional sample highlighting)", "topics": [ "plot_baf_with_ploidy_guides" ] }, { "page": "plot_qploidy_standardization", "title": "Plot Method for Qploidy Standardization", "topics": [ "plot_qploidy_standardization" ] }, { "page": "plot_xy_with_ploidy_guides", "title": "Plot X–Y scatter with ploidy dosage guide lines and optional sample highlighting", "topics": [ "plot_xy_with_ploidy_guides" ] }, { "page": "print.qploidy_area_ploidy_estimation", "title": "print qploidy_area_ploidy_estimation object", "topics": [ "print.qploidy_area_ploidy_estimation" ] }, { "page": "print.qploidy_standardization", "title": "Print method for object of class 'qploidy_standardization'", "topics": [ "print.qploidy_standardization" ] }, { "page": "qploidy_read_vcf", "title": "Convert VCF File to Qploidy Data", "topics": [ "qploidy_read_vcf" ] }, { "page": "read_axiom", "title": "Convert Axiom Array Summary File to Qploidy Input", "topics": [ "read_axiom" ] }, { "page": "read_illumina_array", "title": "Read Illumina Array Files", "topics": [ "read_illumina_array" ] }, { "page": "read_qploidy_standardization", "title": "Read a Qploidy Standardized Dataset (.tsv or .tsv.gz) with format checks", "topics": [ "read_qploidy_standardization" ] }, { "page": "rm_outlier", "title": "Identify and Remove Outliers Based on Bonferroni-Holm Adjusted P-values", "topics": [ "rm_outlier" ] }, { "page": "simulate_axiom_summary", "title": "Simulate an Axiom array summary file", "topics": [ "simulate_axiom_summary" ] }, { "page": "simulate_illumina_file", "title": "Simulate an Illumina File", "topics": [ "simulate_illumina_file" ] }, { "page": "simulate_standardization_input", "title": "Simulate Genotyping Data with Flexible Ploidy", "topics": [ "simulate_standardization_input" ] }, { "page": "simulate_vcf", "title": "Simulate a VCF file with GT, DP, and AD format fields for 2 chromosomes", "topics": [ "simulate_vcf" ] }, { "page": "standardize", "title": "Standardize Allelic Ratio Data and Compute BAF and Z-Scores", "topics": [ "standardize" ] }, { "page": "summary_to_fitpoly", "title": "Convert Summary Data to FitPoly-Compatible Format", "topics": [ "summary_to_fitpoly" ] }, { "page": "updog_centers", "title": "Estimate Centers for Standardization Using Updog Bias", "topics": [ "updog_centers" ] }, { "page": "vcf_sanity_check", "title": "Perform a Sanity Check on a VCF File", "topics": [ "vcf_sanity_check" ] }, { "page": "write_qploidy_standardization", "title": "Write Qploidy Standardization Object to File", "topics": [ "write_qploidy_standardization" ] } ], "_readme": "https://github.com/cristianetaniguti/qploidy/raw/HEAD/README.md", "_rundeps": [ "abind", "ape", "backports", "Biobase", "BiocGenerics", "bit", "bit64", "boot", "broom", "car", "carData", "cli", "cluster", "colorspace", "corrplot", "cowplot", "cpp11", "crayon", "Deriv", "digest", "doBy", "dplyr", "farver", "forecast", "Formula", "fracdiff", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glue", "gridExtra", "gtable", "hms", "isoband", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "memuse", "mgcv", "microbenchmark", "minqa", "modelr", "multtest", "nlme", "nloptr", "nnet", 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object to keep only the known ploidy samples subset", "Array data", "(1) and (2) Standardization", "Recover the ploidy_standardization Object from a Saved File", "(1) and (2) Plot results", "(1) and (2) Ploidy Estimation for All Samples", "Export ploidy result table", "(1) and (2) Save plots for all samples", "(2) Improve standardization selecting a known ploidy subset after first round", "HMM-based Copy Number Estimation and Visualization", "HMM-based Copy Number Estimation", "Parallel HMM Estimation for Multiple Samples", "Summarizing Parallel HMM Results", "Interpreting the CN Track Plot", "Try the Qploidy Shiny App!", "How to cite", "Acknowledgments", "Version 1.0.0", "Versions > 1.0.0" ], "created": "2024-12-20 20:07:45", "modified": "2025-10-14 17:26:27", "commits": 8 } ], "_score": 5.301029995663981, "_indexed": true, "_nocasepkg": "qploidy", "_universes": [ "cristianetaniguti" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.2", "date": 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