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  "Title": "QTL Analysis in Autopolyploid Bi-Parental F1 Populations",
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  "Date": "2024-01-08",
  "Authors@R": "c(person(\"Peter\",\"Bourke\", email = \"pbourkey@gmail.com\", role = c(\"aut\",\"cre\")),\nperson(\"Christine\",\"Hackett\", role = \"ctb\"),\nperson(\"Chris\",\"Maliepaard\", role = \"ctb\"),\nperson(\"Geert\",\"van Geest\", role = \"ctb\"),\nperson(\"Roeland\",\"Voorrips\", role = \"ctb\"),\nperson(\"Johan\",\"Willemsen\", role = \"ctb\"))",
  "Maintainer": "Peter Bourke <pbourkey@gmail.com>",
  "Description": "Quantitative trait loci (QTL) analysis and exploration of\nmeiotic patterns in autopolyploid bi-parental F1 populations.\nFor all ploidy levels, identity-by-descent (IBD) probabilities\ncan be estimated. Significance thresholds, exploring QTL allele\neffects and visualising results are provided. For more\nbackground and to reference the package see\n<doi:10.1093/bioinformatics/btab574>.",
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  "Author": "Peter Bourke [aut, cre], Christine Hackett [ctb], Chris\nMaliepaard [ctb], Geert van Geest [ctb], Roeland Voorrips\n[ctb], Johan Willemsen [ctb]",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://polyploids.r-universe.dev",
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    "count_recombinations",
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    "estimate_IBD",
    "exploreQTL",
    "findPeak",
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    "import_IBD",
    "impute_dosages",
    "maxL_IBD",
    "meiosis_report",
    "plotLinearQTL",
    "plotLinearQTL_list",
    "plotQTL",
    "plotRecLS",
    "PVE",
    "QTLscan",
    "segMaker",
    "singleMarkerRegression",
    "spline_IBD",
    "thinmap",
    "visualiseGIC",
    "visualiseHaplo",
    "visualisePairing",
    "visualiseQTLeffects"
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      "title": "Best Linear Unbiased Estimates of phenotype",
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      "class": [
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      ],
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        "Geno",
        "BLUE"
      ],
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      "table": true,
      "tojson": true
    },
    {
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      "title": "Genotypic Information Coefficient for example tetraploid",
      "object": "GIC_4x",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "IBD_4x",
      "title": "Identical by descent probabilities for example tetraploid",
      "object": "IBD_4x",
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      ],
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      "table": false,
      "tojson": true
    },
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      "object": "mr.ls",
      "class": [
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      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "phased_maplist.4x",
      "title": "Phased maplist for example tetraploid",
      "object": "phased_maplist.4x",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "Phenotypes_4x",
      "title": "Phenotypes for example tetraploid",
      "object": "Phenotypes_4x",
      "class": [
        "data.frame"
      ],
      "fields": [
        "year",
        "geno",
        "pheno"
      ],
      "rows": 150,
      "table": true,
      "tojson": true
    },
    {
      "name": "qtl_LODs.4x",
      "title": "QTL output for example tetraploid",
      "object": "qtl_LODs.4x",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "Rec_Data_4x",
      "title": "Recombination data for example tetraploid",
      "object": "Rec_Data_4x",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "segList_2x",
      "title": "Expected segregation for all markers types of a diploid cross",
      "object": "segList_2x",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "segList_3x",
      "title": "Expected segregation for all markers types of a triploid cross (4 x 2)",
      "object": "segList_3x",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "segList_3x_24",
      "title": "Expected segregation for all markers types of a triploid cross (2 x 4)",
      "object": "segList_3x_24",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "segList_4x",
      "title": "Expected segregation for all markers types of a tetraploid cross",
      "object": "segList_4x",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "segList_6x",
      "title": "Expected segregation for all markers types of a hexaploid cross",
      "object": "segList_6x",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "SNP_dosages.4x",
      "title": "SNP marker dosage data for example tetraploid",
      "object": "SNP_dosages.4x",
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        "array"
      ],
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        "F1_02",
        "F1_03",
        "F1_04",
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        "F1_11",
        "F1_12",
        "F1_13",
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        "F1_15",
        "F1_16",
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        "F1_22",
        "F1_23",
        "F1_24",
        "F1_25",
        "F1_26",
        "F1_27",
        "F1_28",
        "F1_29",
        "F1_30",
        "F1_31",
        "F1_32",
        "F1_33",
        "F1_34",
        "F1_35",
        "F1_36",
        "F1_37",
        "F1_38",
        "F1_39",
        "F1_40",
        "F1_41",
        "F1_42",
        "F1_43",
        "F1_44",
        "F1_45",
        "F1_46",
        "F1_47",
        "F1_48",
        "F1_49",
        "F1_50"
      ],
      "rows": 186,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "BLUE",
      "title": "Calculate Best Linear Unbiased Estimates using linear mixed model from 'nlme' package",
      "topics": [
        "BLUE"
      ]
    },
    {
      "page": "BLUEs.pheno",
      "title": "Best Linear Unbiased Estimates of phenotype",
      "topics": [
        "BLUEs.pheno"
      ]
    },
    {
      "page": "check_cofactors",
      "title": "Build a multi-QTL model using step-wise procedure of checking genetic co-factors.",
      "topics": [
        "check_cofactors"
      ]
    },
    {
      "page": "convert_mappoly_to_phased.maplist",
      "title": "Function to extract the phased map from a mappoly.map object",
      "topics": [
        "convert_mappoly_to_phased.maplist"
      ]
    },
    {
      "page": "count_recombinations",
      "title": "Predict recombination breakpoints using IBD probabilities",
      "topics": [
        "count_recombinations"
      ]
    },
    {
      "page": "estimate_GIC",
      "title": "Estimate the Genotypic Information Coefficient (GIC)",
      "topics": [
        "estimate_GIC"
      ]
    },
    {
      "page": "estimate_IBD",
      "title": "Generate IBD probabilities from marker genotypes and a phased linkage map",
      "topics": [
        "estimate_IBD"
      ]
    },
    {
      "page": "exploreQTL",
      "title": "Explore the possible segregation type of a QTL peak using Schwarz Information Criterion",
      "topics": [
        "exploreQTL"
      ]
    },
    {
      "page": "findPeak",
      "title": "Function to find the position of maximum LOD on a particular linkage group",
      "topics": [
        "findPeak"
      ]
    },
    {
      "page": "findSupport",
      "title": "Function to find a LOD - x support interval around a QTL position",
      "topics": [
        "findSupport"
      ]
    },
    {
      "page": "GIC_4x",
      "title": "Genotypic Information Coefficient for example tetraploid",
      "topics": [
        "GIC_4x"
      ]
    },
    {
      "page": "IBD_4x",
      "title": "Identical by descent probabilities for example tetraploid",
      "topics": [
        "IBD_4x"
      ]
    },
    {
      "page": "import_IBD",
      "title": "Import IBD probabilities as estimated by TetraOrigin or PolyOrigin",
      "topics": [
        "import_IBD"
      ]
    },
    {
      "page": "impute_dosages",
      "title": "Re-estimate marker dosages given IBD input estimated using a high error prior.",
      "topics": [
        "impute_dosages"
      ]
    },
    {
      "page": "maxL_IBD",
      "title": "Wrapper function to run estimate_IBD function over multiple error priors",
      "topics": [
        "maxL_IBD"
      ]
    },
    {
      "page": "meiosis_report",
      "title": "Generate a 'report' of predicted meiotic behaviour in an F1 population",
      "topics": [
        "meiosis_report"
      ]
    },
    {
      "page": "mr.ls",
      "title": "Example output of meiosis report function",
      "topics": [
        "mr.ls"
      ]
    },
    {
      "page": "phased_maplist.4x",
      "title": "Phased maplist for example tetraploid",
      "topics": [
        "phased_maplist.4x"
      ]
    },
    {
      "page": "Phenotypes_4x",
      "title": "Phenotypes for example tetraploid",
      "topics": [
        "Phenotypes_4x"
      ]
    },
    {
      "page": "plotQTL",
      "title": "Plot the results of QTL scan.",
      "topics": [
        "plotLinearQTL",
        "plotLinearQTL_list",
        "plotQTL"
      ]
    },
    {
      "page": "plotRecLS",
      "title": "Plot the recombination landscape across the genome",
      "topics": [
        "plotRecLS"
      ]
    },
    {
      "page": "PVE",
      "title": "Function to determine the percentage variance explained (PVE) of a (maximal) QTL model, and explore sub-models.",
      "topics": [
        "PVE"
      ]
    },
    {
      "page": "qtl_LODs.4x",
      "title": "QTL output for example tetraploid",
      "topics": [
        "qtl_LODs.4x"
      ]
    },
    {
      "page": "QTLscan",
      "title": "General QTL function that allows for co-factors, completely randomised block designs and the possibility to derive LOD thresholds using a permutation test",
      "topics": [
        "QTLscan"
      ]
    },
    {
      "page": "Rec_Data_4x",
      "title": "Recombination data for example tetraploid",
      "topics": [
        "Rec_Data_4x"
      ]
    },
    {
      "page": "segList_2x",
      "title": "Expected segregation for all markers types of a diploid cross",
      "topics": [
        "segList_2x"
      ]
    },
    {
      "page": "segList_3x",
      "title": "Expected segregation for all markers types of a triploid cross (4 x 2)",
      "topics": [
        "segList_3x"
      ]
    },
    {
      "page": "segList_3x_24",
      "title": "Expected segregation for all markers types of a triploid cross (2 x 4)",
      "topics": [
        "segList_3x_24"
      ]
    },
    {
      "page": "segList_4x",
      "title": "Expected segregation for all markers types of a tetraploid cross",
      "topics": [
        "segList_4x"
      ]
    },
    {
      "page": "segList_6x",
      "title": "Expected segregation for all markers types of a hexaploid cross",
      "topics": [
        "segList_6x"
      ]
    },
    {
      "page": "segMaker",
      "title": "Create a list of possible QTL segregation types",
      "topics": [
        "segMaker"
      ]
    },
    {
      "page": "singleMarkerRegression",
      "title": "Run a single marker regression using marker dosages",
      "topics": [
        "singleMarkerRegression"
      ]
    },
    {
      "page": "SNP_dosages.4x",
      "title": "SNP marker dosage data for example tetraploid",
      "topics": [
        "SNP_dosages.4x"
      ]
    },
    {
      "page": "spline_IBD",
      "title": "Fit splines to IBD probabilities",
      "topics": [
        "spline_IBD"
      ]
    },
    {
      "page": "thinmap",
      "title": "Thin out map data",
      "topics": [
        "thinmap"
      ]
    },
    {
      "page": "visualiseGIC",
      "title": "Visualise Genotypic Information Coefficient",
      "topics": [
        "visualiseGIC"
      ]
    },
    {
      "page": "visualiseHaplo",
      "title": "Visualise haplotypes in certain individuals in a certain region",
      "topics": [
        "visualiseHaplo"
      ]
    },
    {
      "page": "visualisePairing",
      "title": "Visualise pairing of parental homologues",
      "topics": [
        "visualisePairing"
      ]
    },
    {
      "page": "visualiseQTLeffects",
      "title": "Visualise QTL homologue effects around a QTL position",
      "topics": [
        "visualiseQTLeffects"
      ]
    }
  ],
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      "source": "polyqtlR_vignette.rmd",
      "filename": "polyqtlR_vignette.html",
      "title": "Performing polyploid QTL analysis using polyqtlR",
      "author": "Peter M. Bourke",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installing polyqtlR",
        "IBD probabilities",
        "Data structures",
        "HMM for IBD estimation",
        "Optional: Importing IBDs from TetraOrigin or PolyOrigin",
        "TetraOrigin",
        "PolyOrigin",
        "\"Heuristic\" method for IBD estimation",
        "High marker densities",
        "Interpolating IBDs",
        "Visualising IBD haplotypes",
        "Genotypic Information",
        "Performing a QTL scan",
        "Including experimental blocks",
        "Running an initial QTL scan",
        "Visualising QTL results",
        "Significance thresholds",
        "BLUEs",
        "Adding genetic co-factors",
        "Manual co-factor analysis",
        "Automatic co-factor analysis",
        "Comparing multiple analyses",
        "Exploring the QTL peak",
        "Compare QTL results with offspring",
        "Single Marker Analysis",
        "PVE",
        "Meiosis & Recombinations",
        "Meiosis report",
        "Preferential pairing",
        "Recombination landscape",
        "Searching for recombinant individuals",
        "Fishing for specific alleles",
        "Correcting genotyping errors",
        "Concluding remarks",
        "References"
      ],
      "created": "2020-12-16 09:40:02",
      "modified": "2024-01-09 02:43:04",
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