{
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  "Version": "1.0.0-10",
  "Date": "2024-01-15",
  "Title": "Correlated Trait Locus Mapping",
  "Author": "Danny Arends <Danny.Arends@gmail.com>, Yang Li, Gudrun A\nBrockmann, Ritsert C Jansen, Robert W Williams, and Pjotr Prins",
  "Maintainer": "Danny Arends <Danny.Arends@gmail.com>",
  "Description": "Identification and network inference of genetic loci\nassociated with correlation changes in quantitative traits\n(called correlated trait loci, CTLs). Arends et al. (2016)\n<doi:10.21105/joss.00087>.",
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    "chiSQtoP",
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    "ctl.qtlprofile",
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    "CTLanalyseRatios",
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    "CTLmapping",
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    "CTLnetwork",
    "CTLnetwork.addmarker",
    "CTLpowerAnalysis",
    "CTLprofiles",
    "CTLregions",
    "CTLscan",
    "CTLscan.cross",
    "CTLscantoScanone",
    "CTLsignificant",
    "CTLtoLODvector",
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    "dcor.create",
    "deltaSD",
    "detect.peaks",
    "draw.element",
    "draw.spline",
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    "getCorrelations.cross",
    "getPermuteThresholds",
    "getRatio",
    "getRVM",
    "hist.CTLobject",
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    "munique",
    "nfrom",
    "nto",
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    "print.CTLpermute",
    "print.CTLscan",
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    "scanSlopes.cross",
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    {
      "page": "ctl-package",
      "title": "CTL - CTL mapping in experimental crosses",
      "topics": [
        "CTL",
        "ctl"
      ]
    },
    {
      "page": "ath.churchill",
      "title": "Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.",
      "topics": [
        "ath.churchill",
        "ath.gary"
      ]
    },
    {
      "page": "ath.metabolites",
      "title": "Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites.",
      "topics": [
        "ath.metab",
        "ath.metabolites"
      ]
    },
    {
      "page": "ath.result",
      "title": "Output of QCLscan after 5000 permutations on the metabolite expression data from Arabidopsis Thaliana.",
      "topics": [
        "ath.result"
      ]
    },
    {
      "page": "basic.qc",
      "title": "Create quality control plots.",
      "topics": [
        "basic.qc"
      ]
    },
    {
      "page": "ctl.circle",
      "title": "Circleplot CTL on multiple traits",
      "topics": [
        "ctl.circle"
      ]
    },
    {
      "page": "ctl.lineplot",
      "title": "Lineplot CTL on multiple traits",
      "topics": [
        "ctl.lineplot"
      ]
    },
    {
      "page": "ctl.load",
      "title": "ctl.load - Load CTLs calculated by the D2.0 version",
      "topics": [
        "ctl.load"
      ]
    },
    {
      "page": "ctl.helper",
      "title": "CTLhelper - Helper functions for CTL mapping",
      "topics": [
        "ctl.ctlmatrix",
        "ctl.dcormatrix",
        "ctl.name",
        "ctl.names",
        "ctl.qtlmatrix",
        "ctl.qtlprofile"
      ]
    },
    {
      "page": "ctl.mapping",
      "title": "CTLmapping - Scan for correlated trait loci (CTL)",
      "topics": [
        "CTLmapping"
      ]
    },
    {
      "page": "ctl.network",
      "title": "CTLnetwork - Interaction network from a genome-wide CTLscan of multiple traits",
      "topics": [
        "CTLnetwork"
      ]
    },
    {
      "page": "ctl.profiles",
      "title": "CTLprofiles - Extract CTL interaction profiles",
      "topics": [
        "CTLprofiles"
      ]
    },
    {
      "page": "ctl.regions",
      "title": "CTLregions - Get all significant interactions from a genome-wide CTLscan",
      "topics": [
        "CTLregions"
      ]
    },
    {
      "page": "ctl.scan",
      "title": "CTLscan - Scan for Correlated Trait Locus (CTL)",
      "topics": [
        "CTLscan"
      ]
    },
    {
      "page": "ctl.scan.cross",
      "title": "CTLscan.cross - Scan for Correlated Trait Locus (CTL) (R/qtl cross object)",
      "topics": [
        "CTLscan.cross"
      ]
    },
    {
      "page": "ctl.significant",
      "title": "CTLsignificant - Get all significant interactions from a genome-wide CTLscan",
      "topics": [
        "CTLsignificant"
      ]
    },
    {
      "page": "detect.peaks",
      "title": "detect.peaks - Peak detection algorithm to 'flatten' data above a certain threshold",
      "topics": [
        "detect.peaks"
      ]
    },
    {
      "page": "ctl.hist",
      "title": "Plot histogram of CTL permutations",
      "topics": [
        "hist.CTLobject"
      ]
    },
    {
      "page": "ctl.image",
      "title": "Plot genome-wide CTL on multiple traits",
      "topics": [
        "image.CTLobject"
      ]
    },
    {
      "page": "ctl.plot.ctlobject",
      "title": "Plot CTL curves or heatmaps",
      "topics": [
        "plot.CTLobject"
      ]
    },
    {
      "page": "ctl.permute.plot",
      "title": "Differential correlation versus likelihood plotted in curves",
      "topics": [
        "plot.CTLpermute"
      ]
    },
    {
      "page": "ctl.plot.ctlscan",
      "title": "Plot CTL results as bar, line or GWAS plot.",
      "topics": [
        "plot.CTLscan"
      ]
    },
    {
      "page": "plotTraits",
      "title": "plotTraits - Trait vs Trait scatterplot, colored by the selected genetic locus",
      "topics": [
        "plotTraits"
      ]
    },
    {
      "page": "ctl.print.ctlobject",
      "title": "Print the results of a CTL genome scan",
      "topics": [
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      ]
    },
    {
      "page": "ctl.print.ctlscan",
      "title": "Print the results of a single phenotype CTL scan",
      "topics": [
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      ]
    },
    {
      "page": "qtl.image",
      "title": "Plot a QTL heatmap of the phenotypes scanned by CTLscan",
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      ]
    },
    {
      "page": "qtl.mapping",
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      ]
    },
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      ]
    },
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      ]
    },
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      ]
    },
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      "page": "scanSlopes.cross",
      "title": "scanSlopes.cross - Create a slope difference profile between two traits (R/qtl cross object)",
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    },
    {
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      "title": "Example gene expression data from Saccharomyces cerevisiae on 301 RNA expressions.",
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