{ "_id": "6a17dd88acfb0bcc41d9c9f4", "Package": "mppR", "Type": "Package", "Version": "1.5.0", "Date": "2024-02-22", "Title": "Multi-Parent Population QTL Analysis", "Authors@R": "c(person(\"Vincent\", \"Garin\", role = c(\"aut\", \"cre\"),\nemail = \"vincent.garin6@gmail.com\",\ncomment = c(ORCID = \"0000-0002-5571-1841\")),\nperson(\"Valentin\", \"Wimmer\", role = c(\"aut\")),\nperson(\"Dietrich\", \"Borchardt\", role = c(\"ctb\", \"dtc\")),\nperson(\"Fred\", \"van Eeuwijk\", role = c(\"ctb\", \"ths\")),\nperson(\"Marcos\", \"Malosetti\", role = c(\"ctb\", \"ths\")))", "Description": "Analysis of experimental multi-parent populations to\ndetect regions of the genome (called quantitative trait loci,\nQTLs) influencing phenotypic traits measured in unique and\nmultiple environments. The population must be composed of\ncrosses between a set of at least three parents (e.g. factorial\ndesign, 'diallel', or nested association mapping). The\nfunctions cover data processing, QTL detection, and results\nvisualization. The implemented methodology is described in\nGarin, Wimmer, Mezmouk, Malosetti and van Eeuwijk (2017)\n, in Garin, Malosetti and van\nEeuwijk (2020) , and in Garin,\nDiallo, Tekete, Thera, ..., and Rami (2024) .", "License": "GPL-3", "RoxygenNote": "7.2.3", "Encoding": "UTF-8", "URL": "https://github.com/vincentgarin/mppR", "BugReports": "https://github.com/vincentgarin/mppR/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://vincentgarin.r-universe.dev", "Date/Publication": "2024-03-11 09:46:38 UTC", "RemoteUrl": "https://github.com/vincentgarin/mppr", "RemoteRef": "HEAD", "RemoteSha": "02e46725613bba39744f877acef672c2fc1ea7db", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 06:08:57 UTC", "User": "root" }, "Author": "Vincent Garin [aut, cre] (ORCID:\n),\nValentin Wimmer [aut],\nDietrich Borchardt [ctb, dtc],\nFred van Eeuwijk [ctb, ths],\nMarcos Malosetti [ctb, ths]", "Maintainer": "Vincent Garin ", "MD5sum": 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"EC_effect", "IBD.mppData", "IBS.mppData", "inc_mat_QTL", "mpp_back_elim", "mpp_CIM", "mpp_CV", "mpp_forward", "mpp_perm", "mpp_proc", "mpp_SIM", "mppData_add_pheno", "mppData_mdf_pheno", "mppGE_CIM", "mppGE_proc", "mppGE_SIM", "MQE_gen_effects", "MQE_proc", "parent_cluster.mppData", "plot_allele_eff_GE", "plot_QxEC", "QC.mppData", "QTL_effect_GE", "QTL_effect_main_QEI", "QTL_effect_main_QxEC", "QTL_forward", "QTL_gen_effects", "QTL_pred_R2", "QTL_R2", "QTL_R2_GE", "QTL_select" ], "_datasets": [ { "name": "mppData", "title": "Complete 'mppData' object", "object": "mppData", "file": "mppData.rda", "class": [ "mppData", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "mppData_GE", "title": "Example 'mppData' object", "object": "mppData_GE", "file": "mppData_GE.rda", "class": [ "mppData", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "mppData_init", "title": "'mppData' object with raw data", "object": "mppData_init", "file": "mppData_init.rda", "class": [ "mppData", "list" ], "fields": [], "table": false, "tojson": true }, { "name": "par_clu", "title": "Parental clustering", "object": "par_clu", "file": "par_clu.rda", "class": [ "matrix", "array" ], "fields": [ "B73", "CML103", "CML322", "CML52", "Hp301", "M37W" ], "rows": 98, "table": true, "tojson": true }, { "name": "USNAM_geno", "title": "Reduced genotype data maize US-NAM population", "object": "USNAM_geno", "file": "USNAM_geno.rda", "class": [ "matrix", "array" ], "fields": [ "L00411", "L00569", "L00068", "L01003", "L00196", "L00609", "L00181", "L00828", "L00454", "L01110", "L00890", "L00254", "L00929", "L01185", "L00659", "L01075", "L00604", "L01015", "L00174", "L00116", "L00707", "L00830", "L00120", "L00410", "L00388", "L00916", "L00356", "L00708", "L00003", "L00585", "L00294", "L00755", "L00368", "L00780", "L00795", "L00048", "L00300", "L01115", "L00736", "L00240", "L00750", "L00082", "L00465", "L00734", "L01174", "L00699", "L00165", "L00588", "L01039", "L01149", "L00210", "L00742", "L01182", "L00553", "L00222", "L00295", "L00158", "L00341", "L00503", "L00138", "L00039", "L01183", "L00194", "L00590", "L00877", "L00139", "L00954", "L01010", "L00492", "L00638", "L00271", "L00851", "L01157", "L00493", "L00437", "L00428", "L00538", "L01134", "L00644", "L00296", "L00516", "L00680", "L00650", "L01188", "L00774", "L00321", "L00824", "L00083", "L00094", "L00766", "L01126", "L00513", "L00842", "L00329", "L00695", "L00284", "L00542", "L00671", "L01121", "L00704", "L01114", "L00834" ], "rows": 506, "table": true, "tojson": true }, { "name": "USNAM_map", "title": "Reduced map maize US-NAM population", "object": "USNAM_map", "file": "USNAM_map.rda", "class": [ "data.frame" ], "fields": [ "mk.names", "chr", "pos.cM" ], "rows": 102, "table": true, "tojson": true }, { "name": "USNAM_pheno", "title": "Reduced phenotype data from Maize US-NAM population", "object": "USNAM_pheno", "file": "USNAM_pheno.rda", "class": [ "matrix", "array" ], "fields": [ "ULA" ], "rows": 500, "table": true, "tojson": true } ], "_help": [ { "page": "create.mppData", "title": "Create a multi-parent population data object", "topics": [ "create.mppData" ] }, { "page": "CV_partition", "title": "Cross validation partition", "topics": [ "CV_partition" ] }, { "page": "design_connectivity", "title": "Connected parts of a MPP design", "topics": [ "design_connectivity" ] }, { "page": "EC_effect", "title": "Determine EC effects", "topics": [ "EC_effect" ] }, { "page": "IBD.mppData", "title": "IBD coding for 'mppData' objects", "topics": [ "IBD.mppData" ] }, { "page": "IBS.mppData", "title": "IBS coding for 'mppData' objects", "topics": [ "IBS.mppData" ] }, { "page": "inc_mat_QTL", "title": "QTL incidence matrix", "topics": [ "inc_mat_QTL" ] }, { "page": "mpp_back_elim", "title": "Backward elimination on QTL candidates", "topics": [ "mpp_back_elim" ] }, { "page": "mpp_CIM", "title": "MPP Composite Interval Mapping", "topics": [ "mpp_CIM" ] }, { "page": "mpp_CV", "title": 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GxE Composite Interval Mapping", "topics": [ "mppGE_CIM" ] }, { "page": "mppGE_proc", "title": "MPP GxE QTL analysis", "topics": [ "mppGE_proc" ] }, { "page": "mppGE_SIM", "title": "MPP GxE Simple Interval Mapping", "topics": [ "mppGE_SIM" ] }, { "page": "MQE_gen_effects", "title": "QTL genetic effects multi-QTL effect model", "topics": [ "MQE_gen_effects" ] }, { "page": "MQE_proc", "title": "Multi-QTL effect MPP analysis", "topics": [ "MQE_proc" ] }, { "page": "par_clu", "title": "Parental clustering", "topics": [ "par_clu" ] }, { "page": "parent_cluster.mppData", "title": "Parent clustering for 'mppData' objects", "topics": [ "parent_cluster.mppData" ] }, { "page": "plot_allele_eff_GE", "title": "plot of genome wide QTL allelic effect significance", "topics": [ "plot_allele_eff_GE" ] }, { "page": "plot_QxEC", "title": "plot QTLxEC effect", "topics": [ "plot_QxEC" ] }, { "page": "plot.QTLprof", "title": "plot QTL profile", "topics": [ "plot.QTLprof" ] }, { "page": "print.summary.mppData", "title": "Print summary.mppData object", "topics": [ "print.summary.mppData" ] }, { "page": "print.summary.QeffRes", "title": "Print summary.QeffRes object", "topics": [ "print.summary.QeffRes" ] }, { "page": "print.summary.QR2Res", "title": "Print summary.QR2Res object", "topics": [ "print.summary.QR2Res" ] }, { "page": "QC.mppData", "title": "Quality control for 'mppData' objects", "topics": [ "QC.mppData" ] }, { "page": "QTL_effect_GE", "title": "MPP GxE QTL genetic effects", "topics": [ "QTL_effect_GE" ] }, { "page": "QTL_effect_main_QEI", "title": "Main and QTL by environment interaction model", "topics": [ "QTL_effect_main_QEI" ] }, { "page": "QTL_effect_main_QxEC", "title": "Estimation of a model with main and QTL by environmental sensitivity terms", "topics": [ "QTL_effect_main_QxEC" ] }, { "page": "QTL_forward", "title": "Forward regression QTL model", "topics": [ "QTL_forward" ] }, { "page": "QTL_gen_effects", "title": "QTL genetic effects", "topics": 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"USNAM_map" ] }, { "page": "USNAM_pheno", "title": "Reduced phenotype data from Maize US-NAM population", "topics": [ "USNAM_pheno" ] } ], "_readme": "https://github.com/vincentgarin/mppr/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "igraph", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "nlme", "pillar", "pkgconfig", "qtl", "R6", "RColorBrewer", "rlang", "S7", "scales", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "mppR_gen_vignette.Rmd", "filename": "mppR_gen_vignette.html", "title": "mppR: An R Package for QTL Analysis in Multi-parent Populations", "author": "Vincent Garin^[Wageningen University, vincent.garin6@gmail.com], Valentin Wimmer^[KWS SAAT SE], Dietriech Borchardt^[KWS SAAT SE], Fred van Eeuwijk^[Wageningen University], Marcos Malosetti^[Wageningen University]", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "Introduction", 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