{ "_id": "6a103120acfb0bcc41c96641", "Package": "mappoly", "Type": "Package", "Title": "Genetic Linkage Maps in Autopolyploids", "Version": "0.4.2", "Authors@R": "c(person(given = \"Marcelo\",\nfamily = \"Mollinari\",\nrole = c(\"aut\", \"cre\"),\nemail = \"marcelo.mollinari@proton.me\",\ncomment = c(ORCID=\"0000-0002-7001-8498\")),\nperson(given = \"Gabriel\",\nfamily = \"Gesteira\",\nrole = \"aut\",\ncomment = c(ORCID=\"0000-0002-4106-7346\")),\nperson(given = \"Cristiane\",\nfamily = \"Taniguti\",\nrole = \"aut\",\ncomment = c(ORCID=\"0000-0002-2021-6883\")),\nperson(given = \"Jeekin\",\nfamily = \"Lau\",\nrole = \"aut\",\ncomment = c(ORCID=\"0000-0003-1114-6892\")),\nperson(given = \"Oscar\",\nfamily = \"Riera-Lizarazu\",\nrole = \"ctb\",\ncomment = c(ORCID=\"0000-0002-7477-4063\")),\nperson(given = \"Guilherme\",\nfamily = \"Pereira\",\nrole = \"ctb\",\ncomment = c(ORCID=\"0000-0002-7106-8630\")),\nperson(given = \"Augusto\",\nfamily = \"Garcia\",\nrole = \"ctb\",\ncomment = c(ORCID=\"0000-0003-0634-3277\")),\nperson(given = \"Zhao-Bang\",\nfamily = \"Zeng\",\nrole = \"ctb\",\ncomment = c(ORCID=\"0000-0002-3115-1149\")),\nperson(given = \"Katharine\",\nfamily = \"Preedy\",\nrole = c(\"ctb\", \"cph\"),\ncomment = \"MDS ordering algorithm\"),\nperson(given = \"Robert\",\nfamily = \"Gentleman\",\nrole = \"cph\",\ncomment = \"C code for MLE optimization in src/pairwise_estimation.cpp\"),\nperson(given = \"Ross\",\nfamily = \"Ihaka\",\nrole = \"cph\",\ncomment = \"C code for MLE optimization in src/pairwise_estimation.cpp\"),\nperson(\"R Core Team\", role = \"cph\",\ncomment = \"Portions of C/C++ code adapted from R sources; see src/pairwise_estimation.cpp\"),\nperson(\"R Foundation for Statistical Computing\", role = \"cph\",\ncomment = \"Portions of C/C++ code adapted from R sources; see src/pairwise_estimation.cpp\"))", "Maintainer": "Marcelo Mollinari ", "Description": "Constructs genetic linkage maps in autopolyploid full-sib\npopulations. Uses pairwise recombination fraction estimation as\nthe first source of information to sequentially position\nallelic variants in specific homologous chromosomes. For\nsituations where pairwise analysis has limited power, the\nalgorithm relies on the multilocus likelihood obtained through\na hidden Markov model (HMM). Methods are described in Mollinari\nand Garcia (2019) and Mollinari et\nal. (2020) .", "License": "GPL-3", "LazyData": "TRUE", "LazyDataCompression": "xz", "RoxygenNote": "7.3.3", "SystemRequirements": "GNU make", "Encoding": "UTF-8", "URL": "https://github.com/mmollina/MAPpoly", "BugReports": "https://github.com/mmollina/MAPpoly/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nlibx11-dev zlib1g-dev", "Repository": "https://mmollina.r-universe.dev", "Date/Publication": "2026-01-12 01:15:11 UTC", "RemoteUrl": "https://github.com/mmollina/mappoly", "RemoteRef": "HEAD", "RemoteSha": "09ec30a58a6b9d4b6edc8bc6af44021c94bb7ec0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-12 09:21:38 UTC", "User": "root" }, "Author": "Marcelo Mollinari [aut, cre] (ORCID:\n),\nGabriel Gesteira [aut] (ORCID: ),\nCristiane Taniguti [aut] (ORCID:\n),\nJeekin Lau [aut] (ORCID: ),\nOscar Riera-Lizarazu [ctb] (ORCID:\n),\nGuilherme Pereira [ctb] (ORCID:\n),\nAugusto Garcia [ctb] (ORCID: ),\nZhao-Bang Zeng [ctb] (ORCID: 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genotypes using probability distribution of dosages", "topics": [ "calc_genoprob_dist" ] }, { "page": "calc_genoprob_error", "title": "Compute conditional probabilities of the genotypes using global error", "topics": [ "calc_genoprob_error" ] }, { "page": "calc_genoprob_single_parent", "title": "Compute conditional probabilities of the genotype (one informative parent)", "topics": [ "calc_genoprob_single_parent" ] }, { "page": "calc_homologprob", "title": "Homolog probabilities", "topics": [ "calc_homologprob" ] }, { "page": "calc_prefpair_profiles", "title": "Preferential pairing profiles", "topics": [ "calc_prefpair_profiles" ] }, { "page": "check_data_sanity", "title": "Data sanity check", "topics": [ "check_data_sanity" ] }, { "page": "compare_maps", "title": "Compare a list of maps", "topics": [ "compare_maps" ] }, { "page": "cross_simulate", "title": "Simulate an autopolyploid full-sib population", "topics": [ "cross_simulate" ] }, { "page": "detect_info_par", "title": "Detects which parent is informative", "topics": [ "detect_info_par" ] }, { "page": "drop_marker", "title": "Remove markers from a map", "topics": [ "drop_marker" ] }, { "page": "edit_order", "title": "Edit sequence ordered by reference genome positions comparing to another set order", "topics": [ "edit_order" ] }, { "page": "elim_redundant", "title": "Eliminate redundant markers", "topics": [ "elim_redundant" ] }, { "page": "est_full_hmm_with_global_error", "title": "Re-estimate genetic map given a global genotyping error", "topics": [ "est_full_hmm_with_global_error" ] }, { "page": "est_full_hmm_with_prior_prob", "title": "Re-estimate genetic map using dosage prior probability distribution", "topics": [ "est_full_hmm_with_prior_prob" ] }, { "page": "est_pairwise_rf", "title": "Pairwise two-point analysis", "topics": [ "est_pairwise_rf" ] }, { "page": "est_pairwise_rf2", "title": "Pairwise two-point analysis - RcppParallel version", "topics": [ "est_pairwise_rf2" ] }, { "page": "est_rf_hmm", "title": "Multipoint analysis using Hidden Markov Models in autopolyploids", "topics": [ "est_rf_hmm", "plot.mappoly.map", "print.mappoly.map" ] }, { "page": "est_rf_hmm_sequential", "title": "Multipoint analysis using Hidden Markov Models: Sequential phase elimination", "topics": [ "est_rf_hmm_sequential" ] }, { "page": "export_data_to_polymapR", "title": "Export data to 'polymapR'", "topics": [ "export_data_to_polymapR" ] }, { "page": "export_map_list", "title": "Export a genetic map to a CSV file", "topics": [ "export_map_list" ] }, { "page": "export_qtlpoly", "title": "Export to QTLpoly", "topics": [ "export_qtlpoly" ] }, { "page": "extract_map", "title": "Extract the maker position from an object of class 'mappoly.map'", "topics": [ "extract_map" ] }, { "page": "filter_aneuploid", "title": "Filter aneuploid chromosomes from progeny individuals", "topics": [ "filter_aneuploid" ] }, { "page": "filter_individuals", "title": "Filter out individuals", "topics": [ "filter_individuals" ] }, { "page": "filter_missing", "title": "Filter missing genotypes", "topics": [ "filter_missing" ] }, { "page": "filter_segregation", "title": "Filter markers based on chi-square test", "topics": [ "filter_segregation" ] }, { "page": "find_blocks", "title": "Allocate markers into linkage blocks", "topics": [ "find_blocks" ] }, { "page": "framework_map", "title": "Design linkage map framework in two steps: i) estimating the recombination fraction with HMM approach for each parent separately using only markers segregating individually (e.g. map 1 - P1:3 x P2:0, P1: 2x4; map 2 - P1:0 x P2:3, P1:4 x P2:2); ii) merging both maps and re-estimate recombination fractions.", "topics": [ "framework_map" ] }, { "page": "genetic-mapping-functions", "title": "Genetic Mapping Functions", "topics": [ "genetic-mapping-functions", "imf_h", "imf_k", "imf_m", "mf_h", "mf_k", "mf_m" ] }, { "page": "get_genomic_order", "title": "Get the genomic position of markers in a sequence", "topics": [ 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