{ "_id": "6a23c786530b9bc726be0636", "Package": "qtl", "Version": "1.74", "Date": "2025-12-08", "Title": "Tools for Analyzing QTL Experiments", "Author": "Karl W Broman [aut, cre] (ORCID:\n), Hao Wu [aut], Gary\nChurchill [ctb] (ORCID:\n), Saunak Sen [ctb]\n(ORCID: ), Danny Arends\n[ctb] (ORCID: ), Robert\nCorty [ctb], Timothee Flutre [ctb], Ritsert Jansen [ctb], Pjotr\nPrins [ctb] (ORCID: ),\nLars Ronnegard [ctb], Rohan Shah [ctb], Laura Shannon [ctb],\nQuoc Tran [ctb], Aaron Wolen [ctb], Brian Yandell [ctb] (ORCID:\n), R Core Team [ctb]", "Authors@R": "c(person(given = c(\"Karl\", \"W\"),\nfamily = \"Broman\",\nrole = c(\"aut\", \"cre\"),\nemail = \"broman@wisc.edu\",\ncomment=c(ORCID = \"0000-0002-4914-6671\")),\nperson(given = \"Hao\",\nfamily = \"Wu\",\nrole = \"aut\"),\nperson(given = c(\"Gary\"),\nfamily = \"Churchill\",\nrole = \"ctb\",\ncomment=c(ORCID = \"0000-0001-9190-9284\")),\nperson(given = \"Saunak\",\nfamily = \"Sen\",\nrole = \"ctb\",\ncomment=c(ORCID = \"0000-0003-4519-6361\")),\nperson(given = \"Danny\",\nfamily = \"Arends\",\nrole = \"ctb\",\ncomment=c(ORCID = \"0000-0001-8738-0162\")),\nperson(given = \"Robert\",\nfamily = \"Corty\",\nrole = \"ctb\"),\nperson(given = \"Timothee\",\nfamily = \"Flutre\",\nrole = \"ctb\"),\nperson(given = \"Ritsert\",\nfamily = \"Jansen\",\nrole = \"ctb\"),\nperson(given = \"Pjotr\",\nfamily = \"Prins\",\nrole = \"ctb\",\ncomment=c(ORCID = \"0000-0002-8021-9162\")),\nperson(given = \"Lars\",\nfamily = \"Ronnegard\",\nrole = \"ctb\"),\nperson(given = \"Rohan\",\nfamily = \"Shah\",\nrole = \"ctb\"),\nperson(given = \"Laura\",\nfamily = \"Shannon\",\nrole = \"ctb\"),\nperson(given = \"Quoc\",\nfamily = \"Tran\",\nrole = \"ctb\"),\nperson(given = \"Aaron\",\nfamily = \"Wolen\",\nrole = \"ctb\"),\nperson(given = \"Brian\",\nfamily = \"Yandell\",\nrole = \"ctb\",\ncomment=c(ORCID = \"0000-0002-8774-9377\")),\nperson(\"R Core Team\",\nrole = \"ctb\"))", "Maintainer": "Karl W Broman ", "Description": "Analysis of experimental crosses to identify genes (called\nquantitative trait loci, QTLs) contributing to variation in\nquantitative traits. 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"page": "fill.geno", "title": "Fill holes in genotype data", "topics": [ "fill.geno" ] }, { "page": "find_large_intervals", "title": "Find large intervals in a map", "topics": [ "find_large_intervals" ] }, { "page": "find.flanking", "title": "Find flanking markers for a specified position", "topics": [ "find.flanking" ] }, { "page": "find.marker", "title": "Find marker closest to a specified position", "topics": [ "find.marker" ] }, { "page": "findmarkerindex", "title": "Determine the numeric index for a marker", "topics": [ "find.markerindex" ] }, { "page": "find.markerpos", "title": "Find position of a marker", "topics": [ "find.markerpos" ] }, { "page": "find.pheno", "title": "Find column number for a particular phenotype", "topics": [ "find.pheno" ] }, { "page": "find.pseudomarker", "title": "Find the pseudomarker closest to a specified position", "topics": [ "find.pseudomarker" ] }, { "page": "findDupMarkers", "title": "Find markers with identical genotype data", "topics": [ "findDupMarkers" ] }, { "page": "fitqtl", "title": "Fit a multiple-QTL model", "topics": [ "fitqtl" ] }, { "page": "fitstahl", "title": "Fit Stahl interference model", "topics": [ "fitstahl" ] }, { "page": "flip.order", "title": "Flip the orders of markers on a set of chromosomes", "topics": [ "flip.order" ] }, { "page": "formLinkageGroups", "title": "Partition markers into linkage groups", "topics": [ "formLinkageGroups" ] }, { "page": "formMarkerCovar", "title": "Create matrix of marker covariates for QTL analysis", "topics": [ "formMarkerCovar" ] }, { "page": "geno.crosstab", "title": "Create table of two-locus genotypes", "topics": [ "geno.crosstab" ] }, { "page": "geno.image", "title": "Plot grid of genotype data", "topics": [ "geno.image" ] }, { "page": "geno.table", "title": "Create table of genotype distributions", "topics": [ "geno.table" ] }, { "page": "getid", "title": "Pull out the individual identifiers from a cross", "topics": [ "getid" ] }, { "page": "groupclusteredheatmap", "title": "Retrieving groups of traits after clustering", "topics": [ "groupclusteredheatmap" ] }, { "page": "hyper", "title": "Data on hypertension", "topics": [ "hyper" ] }, { "page": "inferFounderHap", "title": "Crude reconstruction of founder haplotypes in multi-parent RIL", "topics": [ "inferFounderHap" ] }, { "page": "inferredpartitions", "title": "Identify inferred partitions in mapping QTL to a phylogenetic tree", "topics": [ "inferredpartitions" ] }, { "page": "interpPositions", "title": "Interpolate positions from one map to another", "topics": [ "interpPositions" ] }, { "page": "jittermap", "title": "Jitter marker positions in a genetic map", "topics": [ "jittermap" ] }, { "page": "listeria", "title": "Data on Listeria monocytogenes susceptibility", "topics": [ "listeria" ] }, { "page": "locateXO", "title": "Estimate locations of crossovers", "topics": [ "locateXO" ] }, { "page": "locations", "title": "Genetic locations of traits for the multitrait dataset", "topics": [ "locations" ] }, { "page": "lodint", "title": "LOD support interval", "topics": [ "lodint" ] }, { "page": "makeqtl", "title": "Make a qtl object", "topics": [ "makeqtl" ] }, { "page": "map10", "title": "An example genetic map", "topics": [ "map10" ] }, { "page": "map2table", "title": "Convert genetic map from list to table.", "topics": [ "map2table" ] }, { "page": "mapthis", "title": "Simulated data for illustrating genetic map construction", "topics": [ "mapthis" ] }, { "page": "markerlrt", "title": "General likelihood ratio test for association between marker pairs", "topics": [ "markerlrt" ] }, { "page": "markernames", "title": "Pull out the marker names from a cross", "topics": [ "markernames" ] }, { "page": "max.scanone", "title": "Maximum peak in genome scan", "topics": [ "max.scanone" ] }, { "page": "max.scanPhyloQTL", "title": "Maximum peak in genome scan to map a QTL to a phylogenetic tree", "topics": [ "max.scanPhyloQTL" ] }, { "page": "max.scantwo", "title": "Maximum peak in two-dimensional genome scan", "topics": [ "max.scantwo" ] }, { "page": "movemarker", "title": "Move a marker to a new chromosome", "topics": [ "movemarker" ] }, { "page": "MQM", "title": "Introduction to Multiple QTL Model (MQM) mapping", "topics": [ "MQM" ] }, { "page": "mqmaugment", "title": "MQM augmentation", "topics": [ "mqmaugment" ] }, { "page": "mqmautocofactors", "title": "Automatic setting of cofactors, taking marker density into account", "topics": [ "mqmautocofactors" ] }, { "page": "mqmextractmarkers", "title": "MQM marker extraction", "topics": [ "mqmextractmarkers" ] }, { "page": "mqmfind.marker", "title": "Fetch significant markers after permutation analysis", "topics": [ "mqmfind.marker" ] }, { "page": "mqmgetmodel", "title": "Retrieve the QTL model used in mapping from the results of an MQM scan", "topics": [ "mqmgetmodel" ] }, { "page": "mqmpermutation", "title": "Estimate QTL LOD score significance using permutations or simulations", "topics": [ "mqmpermutation" ] }, { "page": "mqmplotcircle", "title": "Circular genome plot for MQM", "topics": [ "mqmplot.circle" ] }, { "page": "mqmplotcistrans", "title": "cis-trans plot", "topics": [ "mqmplot.cistrans" ] }, { "page": "mqmplotclusteredheatmap", "title": "Plot clustered heatmap of MQM scan on multiple phenotypes", "topics": [ "mqmplot.clusteredheatmap" ] }, { "page": "mqmplotcofactors", "title": "Plot cofactors on the genetic map", "topics": [ "mqmplot.cofactors" ] }, { "page": "mqmplotdirectedqtl", "title": "Plot LOD*Effect curves of a multiple-QTL model", "topics": [ "mqmplot.directedqtl" ] }, { "page": "mqmplotheatmap", "title": "Heatmap of a genome of MQM scan on multiple phenotypes", "topics": [ "mqmplot.heatmap" ] }, { "page": "mqmplotmultitrait", "title": "Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes", "topics": [ "mqmplot.multitrait" ] }, { "page": "mqmplotpermutations", "title": "Plot results from mqmpermutation", "topics": [ "mqmplot.permutations" ] }, { "page": "mqmplotsingletrait", "title": "Plot LOD curves of a multiple-QTL model", "topics": [ "mqmplot.singletrait" ] }, { "page": "mqmprocesspermutation", "title": "Convert mqmmulti objects into a scanoneperm object", "topics": [ "mqmprocesspermutation" ] }, { "page": "mqmscan", "title": "Genome scan with a multiple QTL model (MQM)", "topics": [ "mqmscan" ] }, { "page": "mqmscanall", "title": "Parallelized MQM on multiple phenotypes in a cross object", "topics": [ "mqmscanall" ] }, { "page": "mqmscanfdr", "title": "Estimate FDR for multiple trait QTL analysis", "topics": [ "mqmscanfdr" ] }, { "page": "mqmsetcofactors", "title": "Set cofactors at fixed intervals, to be used with MQM", "topics": [ "mqmsetcofactors" ] }, { "page": "mqmtestnormal", "title": "Shapiro normality test used for MQM", "topics": [ "mqmtestnormal" ] }, { "page": "multitrait", "title": "Example Cross object from R/QTL with multiple traits", "topics": [ "multitrait" ] }, { "page": "nchr", "title": "Determine the number of chromosomes", "topics": [ "nchr" ] }, { "page": "nind", "title": "Determine the number of individuals QTL experiment", "topics": [ "nind" ] }, { "page": "nmar", "title": "Determine the numbers of markers on each chromosome", "topics": [ "nmar" ] }, { "page": "nmissing", "title": "Number of missing genotypes", "topics": [ "nmissing" ] }, { "page": "nphe", "title": "Determine the number of phenotypes QTL experiment", "topics": [ "nphe" ] }, { "page": "nqrank", "title": "Transform a vector of quantitative values to the corresponding normal quantiles", "topics": [ "nqrank" ] }, { "page": "nqtl", "title": "Determine the number of QTL in a QTL object", "topics": [ "nqtl" ] }, { "page": "ntyped", "title": "Number of genotypes", "topics": [ "ntyped" ] }, { "page": "nullmarkers", "title": "Identify markers without any genotype data", "topics": [ "nullmarkers" ] }, { "page": "orderMarkers", "title": "Find an initial order for markers within chromosomes", "topics": [ "orderMarkers" ] }, { "page": "phenames", "title": "Pull out the phenotypes names from a cross", "topics": [ "phenames" ] }, { "page": "pickMarkerSubset", "title": "Identify the largest subset of markers that are some distance apart", "topics": [ "pickMarkerSubset" ] }, { "page": "plot.comparegeno", "title": "Plot genotype comparison", "topics": [ "plot.comparegeno" ] }, { "page": "plot.cross", "title": "Plot various features of a cross object", "topics": [ "plot.cross" ] }, { "page": "plot.qtl", "title": "Plot QTL locations", "topics": [ "plot.qtl" ] }, { "page": "plot.rfmatrix", "title": "Plot recombination fractions or LOD scores for a single marker", "topics": [ "plot.rfmatrix" ] }, { "page": "plot.scanone", "title": "Plot LOD curves", "topics": [ "plot.scanone" ] }, { "page": "plot.scanoneboot", "title": "Plot results of bootstrap for QTL position", "topics": [ "plot.scanoneboot" ] }, { "page": "plot.scanoneperm", "title": "Plot permutation results for a single-QTL genome scan", "topics": [ "plot.scanoneperm" ] }, { "page": "plot.scanPhyloQTL", "title": "Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree", "topics": [ "plot.scanPhyloQTL" ] }, { "page": "plot.scantwo", "title": "Plot LOD scores for a two-dimensional genome scan", "topics": [ "plot.scantwo" ] }, { "page": "plot.scantwoperm", "title": "Plot permutation results for a 2d, 2-QTL genome scan", "topics": [ "plot.scantwoperm" ] }, { "page": "plot.errorlod", "title": "Plot grid of error LOD values", "topics": [ "plotErrorlod" ] }, { "page": "plot.geno", "title": "Plot observed genotypes, flagging likely errors", "topics": [ "plotGeno" ] }, { "page": "plot.info", "title": "Plot the proportion of missing genotype information", "topics": [ "plotInfo" ] }, { "page": "plotLodProfile", "title": "Plot 1-d LOD profiles for a multiple QTL model", "topics": [ "plotLodProfile" ] }, { "page": "plot.map", "title": "Plot genetic map", "topics": [ "plot.map", "plotMap" ] }, { "page": "plot.missing", "title": "Plot grid of missing genotypes", "topics": [ "plotMissing" ] }, { "page": "plotModel", "title": "Plot a QTL model", "topics": [ "plotModel" ] }, { "page": "plot.pheno", "title": "Plot a phenotype distribution", "topics": [ "plotPheno" ] }, { "page": "plot.pxg", "title": "Plot phenotypes versus marker genotypes", "topics": [ "plotPXG" ] }, { "page": "plot.rf", "title": "Plot recombination fractions", "topics": [ "plotRF" ] }, { "page": "pull.argmaxgeno", "title": "Pull out the results of the Viterbi algorithm from a cross", "topics": [ "pull.argmaxgeno" ] }, { "page": "pull.draws", "title": "Pull out the genotype imputations from a cross", "topics": [ "pull.draws" ] }, { "page": "pull.geno", "title": "Pull out the genotype data from a cross", "topics": [ "pull.geno" ] }, { "page": "pull.genoprob", "title": "Pull out the genotype probabilities from a cross", "topics": [ "pull.genoprob" ] }, { "page": "pull.map", "title": "Pull out the genetic map from a cross", "topics": [ "pull.map" ] }, { "page": "pull.markers", "title": "Drop all but a selected set of markers", "topics": [ "pull.markers" ] }, { "page": "pull.pheno", "title": "Pull out phenotype data from a cross", "topics": [ "pull.pheno" ] }, { "page": "pull.rf", "title": "Pull out recombination fractions or LOD scores from a cross object", "topics": [ "pull.rf" ] }, { "page": "qtlversion", "title": "Installed version of R/qtl", "topics": [ "qtlversion" ] }, { "page": "read.cross", "title": "Read data for a QTL experiment", "topics": [ "read.cross" ] }, { "page": "readMWril", "title": "Read data for 4- or 8-way RIL", "topics": [ "readMWril" ] }, { "page": "reduce2grid", "title": "Reduce to a grid of pseudomarkers.", "topics": [ "reduce2grid" ] }, { "page": "refineqtl", "title": "Refine the positions of QTL", "topics": [ "refineqtl" ] }, { "page": "reorderqtl", "title": "Reorder the QTL in a qtl object", "topics": [ "reorderqtl" ] }, { "page": "replace.map", "title": "Replace the genetic map of a cross", "topics": [ "replace.map", "replacemap.cross" ] }, { "page": "replacemap.scanone", "title": "Replace the genetic map in QTL mapping results with an alternate map", "topics": [ "replacemap.scanone" ] }, { "page": "replacemap.scantwo", "title": "Replace the genetic map in QTL mapping results with an alternate map", "topics": [ "replacemap.scantwo" ] }, { "page": "replaceqtl", "title": "Replace a QTL in a qtl object with a different position", "topics": [ "replaceqtl" ] }, { "page": "rescalemap", "title": "Rescale genetic maps", "topics": [ "rescalemap" ] }, { "page": "ripple", "title": "Compare marker orders", "topics": [ "ripple" ] }, { "page": "scanone", "title": "Genome scan with a single QTL model", "topics": [ "scanone" ] }, { "page": "scanoneboot", "title": "Bootstrap to get interval estimate of QTL location", "topics": [ "scanoneboot" ] }, { "page": "scanonevar", "title": "Genome scan for QTL affecting mean and/or variance", "topics": [ "scanonevar" ] }, { "page": "scanonevar.meanperm", "title": "Permutation test for mean effect in scanonevar", "topics": [ "scanonevar.meanperm" ] }, { "page": "scanonevar.varperm", "title": "Permutation test for variance effect in scanonevar", "topics": [ "scanonevar.varperm" ] }, { "page": "scanPhyloQTL", "title": "Single-QTL genome scan to map QTL to a phylogenetic tree", "topics": [ "scanPhyloQTL" ] }, { "page": "scanqtl", "title": "General QTL scan", "topics": [ "scanqtl" ] }, { "page": "scantwo", "title": "Two-dimensional genome scan with a two-QTL model", "topics": [ "scantwo" ] }, { "page": "scantwopermhk", "title": "Permutation test for 2d genome scan by Haley-Knott regression", "topics": [ "scantwopermhk" ] }, { "page": "shiftmap", "title": "Shift starting points in genetic maps", "topics": [ "shiftmap" ] }, { "page": "sim.cross", "title": "Simulate a QTL experiment", "topics": [ "sim.cross" ] }, { "page": "sim.geno", "title": "Simulate genotypes given observed marker data", "topics": [ "sim.geno" ] }, { "page": "sim.map", "title": "Simulate a genetic map", "topics": [ "sim.map" ] }, { "page": "simFounderSnps", "title": "Simulate founder SNPs for a multiple-strain RIL", "topics": [ "simFounderSnps" ] }, { "page": "simPhyloQTL", "title": "Simulate a set of intercrosses for a single diallelic QTL", "topics": [ "simPhyloQTL" ] }, { "page": "simulateMissingData", "title": "Simulates missing genotype data", "topics": [ "simulatemissingdata" ] }, { "page": "stepwiseqtl", "title": "Stepwise selection for multiple QTL", "topics": [ "stepwiseqtl" ] }, { "page": "strip.partials", "title": "Strip partially informative genotypes", "topics": [ "strip.partials" ] }, { "page": "subset.cross", "title": "Subsetting data for QTL experiment", "topics": [ "subset.cross", "[.cross" ] }, { "page": "subset.map", "title": "Subsetting chromosomes for a genetic map", "topics": [ "subset.map", "[.map" ] }, { "page": "subset.scanone", "title": "Subsetting the results of a genome scan", "topics": 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