| Introductory comments on R/qtl | qtl-package |
| Indicate marker covariates from composite interval mapping | add.cim.covar |
| Add significance threshold to plot | add.threshold |
| Add QTL x covariate interaction to a multiple-QTL model | addcovarint |
| Add pairwise interaction to a multiple-QTL model | addint |
| Add phenotype location into a cross object | addloctocross |
| Add a marker to a cross | addmarker |
| Scan for an additional pair of QTL in a multiple-QTL model | addpair |
| Scan for an additional QTL in a multiple-QTL model | addqtl |
| Add to a qtl object | addtoqtl |
| Test all possible splits of a chromosome into two pieces | allchrsplits |
| Reconstruct underlying genotypes | argmax.geno |
| Arithmetic operators for scanone and scantwo results | +.scanone +.scantwo -.scanone -.scantwo |
| Arithmetic Operators for permutation results | +.scanoneperm +.scantwoperm -.scanoneperm -.scantwoperm |
| An intercross with misplaced markers | badorder |
| Bayesian credible interval | bayesint |
| Data on bristle number in Drosophila | bristle3 |
| Data on bristle number in Drosophila | bristleX |
| Combine data for QTL experiments | c.cross |
| Combine columns from multiple scanone results | c.scanone cbind.scanone |
| Combine data from scanone permutations | c.scanoneperm rbind.scanoneperm |
| Combine columns from multiple scantwo results | c.scantwo cbind.scantwo |
| Combine data from scantwo permutations | c.scantwoperm rbind.scantwoperm |
| Identify likely genotyping errors | calc.errorlod |
| Calculate conditional genotype probabilities | calc.genoprob |
| Calculate LOD penalties | calc.penalties |
| Combine columns from multiple scanone permutation results | cbind.scanoneperm |
| Combine scantwo permutations by column | cbind.scantwoperm |
| Identify markers with switched alleles | checkAlleles |
| Chromosome lengths in QTL experiment | chrlen |
| Pull out the chromosome names from a cross | chrnames |
| Composite interval mapping | cim |
| Remove derived data | clean.cross |
| Clean up scantwo output | clean.scantwo |
| Delete genotypes that are possibly in error | cleanGeno |
| Compare two cross objects | comparecrosses |
| Compare individuals' genotype data | comparegeno |
| Compare two orderings of markers on a chromosome | compareorder |
| Condense the output from a 2-d genome scan | condense.scantwo |
| Change map function for a genetic map | convert.map |
| Convert output from scanone for R/qtl version 0.98 | convert.scanone |
| Convert output from scantwo for R/qtl version 1.03 and earlier | convert.scantwo |
| Convert a cross to RIL by selfing | convert2riself |
| Convert a cross to RIL by sib mating | convert2risib |
| Convert a sex-specific map to a sex-averaged one | convert2sa |
| Count number of obligate crossovers for each individual | countXO |
| Drop duplicate markers | drop.dupmarkers |
| Drop a set of markers | drop.markers |
| Drop markers without any genotype data | drop.nullmarkers |
| Drop a QTL from a qtl object | dropfromqtl |
| Drop one marker at a time and determine effect on genetic map | droponemarker |
| Plot phenotype means against genotypes at one or two markers | effectplot |
| Plot estimated QTL effects across the whole genome | effectscan |
| Estimate genetic maps | est.map |
| Estimate pairwise recombination fractions | est.rf |
| Simulated data for a 4-way cross | fake.4way |
| Simulated data for a backcross | fake.bc |
| Simulated data for an F2 intercross | fake.f2 |
| Fill holes in genotype data | fill.geno |
| Find large intervals in a map | find_large_intervals |
| Find flanking markers for a specified position | find.flanking |
| Find marker closest to a specified position | find.marker |
| Determine the numeric index for a marker | find.markerindex |
| Find position of a marker | find.markerpos |
| Find column number for a particular phenotype | find.pheno |
| Find the pseudomarker closest to a specified position | find.pseudomarker |
| Find markers with identical genotype data | findDupMarkers |
| Fit a multiple-QTL model | fitqtl |
| Fit Stahl interference model | fitstahl |
| Flip the orders of markers on a set of chromosomes | flip.order |
| Partition markers into linkage groups | formLinkageGroups |
| Create matrix of marker covariates for QTL analysis | formMarkerCovar |
| Create table of two-locus genotypes | geno.crosstab |
| Plot grid of genotype data | geno.image |
| Create table of genotype distributions | geno.table |
| Pull out the individual identifiers from a cross | getid |
| Retrieving groups of traits after clustering | groupclusteredheatmap |
| Data on hypertension | hyper |
| Crude reconstruction of founder haplotypes in multi-parent RIL | inferFounderHap |
| Identify inferred partitions in mapping QTL to a phylogenetic tree | inferredpartitions |
| Interpolate positions from one map to another | interpPositions |
| Jitter marker positions in a genetic map | jittermap |
| Data on Listeria monocytogenes susceptibility | listeria |
| Estimate locations of crossovers | locateXO |
| Genetic locations of traits for the multitrait dataset | locations |
| LOD support interval | lodint |
| Make a qtl object | makeqtl |
| An example genetic map | map10 |
| Convert genetic map from list to table. | map2table |
| Simulated data for illustrating genetic map construction | mapthis |
| General likelihood ratio test for association between marker pairs | markerlrt |
| Pull out the marker names from a cross | markernames |
| Maximum peak in genome scan | max.scanone |
| Maximum peak in genome scan to map a QTL to a phylogenetic tree | max.scanPhyloQTL |
| Maximum peak in two-dimensional genome scan | max.scantwo |
| Move a marker to a new chromosome | movemarker |
| Introduction to Multiple QTL Model (MQM) mapping | MQM |
| MQM augmentation | mqmaugment |
| Automatic setting of cofactors, taking marker density into account | mqmautocofactors |
| MQM marker extraction | mqmextractmarkers |
| Fetch significant markers after permutation analysis | mqmfind.marker |
| Retrieve the QTL model used in mapping from the results of an MQM scan | mqmgetmodel |
| Estimate QTL LOD score significance using permutations or simulations | mqmpermutation |
| Circular genome plot for MQM | mqmplot.circle |
| cis-trans plot | mqmplot.cistrans |
| Plot clustered heatmap of MQM scan on multiple phenotypes | mqmplot.clusteredheatmap |
| Plot cofactors on the genetic map | mqmplot.cofactors |
| Plot LOD*Effect curves of a multiple-QTL model | mqmplot.directedqtl |
| Heatmap of a genome of MQM scan on multiple phenotypes | mqmplot.heatmap |
| Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes | mqmplot.multitrait |
| Plot results from mqmpermutation | mqmplot.permutations |
| Plot LOD curves of a multiple-QTL model | mqmplot.singletrait |
| Convert mqmmulti objects into a scanoneperm object | mqmprocesspermutation |
| Genome scan with a multiple QTL model (MQM) | mqmscan |
| Parallelized MQM on multiple phenotypes in a cross object | mqmscanall |
| Estimate FDR for multiple trait QTL analysis | mqmscanfdr |
| Set cofactors at fixed intervals, to be used with MQM | mqmsetcofactors |
| Shapiro normality test used for MQM | mqmtestnormal |
| Example Cross object from R/QTL with multiple traits | multitrait |
| Determine the number of chromosomes | nchr |
| Determine the number of individuals QTL experiment | nind |
| Determine the numbers of markers on each chromosome | nmar |
| Number of missing genotypes | nmissing |
| Determine the number of phenotypes QTL experiment | nphe |
| Transform a vector of quantitative values to the corresponding normal quantiles | nqrank |
| Determine the number of QTL in a QTL object | nqtl |
| Number of genotypes | ntyped |
| Identify markers without any genotype data | nullmarkers |
| Find an initial order for markers within chromosomes | orderMarkers |
| Pull out the phenotypes names from a cross | phenames |
| Identify the largest subset of markers that are some distance apart | pickMarkerSubset |
| Plot genotype comparison | plot.comparegeno |
| Plot various features of a cross object | plot.cross |
| Plot QTL locations | plot.qtl |
| Plot recombination fractions or LOD scores for a single marker | plot.rfmatrix |
| Plot LOD curves | plot.scanone |
| Plot results of bootstrap for QTL position | plot.scanoneboot |
| Plot permutation results for a single-QTL genome scan | plot.scanoneperm |
| Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree | plot.scanPhyloQTL |
| Plot LOD scores for a two-dimensional genome scan | plot.scantwo |
| Plot permutation results for a 2d, 2-QTL genome scan | plot.scantwoperm |
| Plot grid of error LOD values | plotErrorlod |
| Plot observed genotypes, flagging likely errors | plotGeno |
| Plot the proportion of missing genotype information | plotInfo |
| Plot 1-d LOD profiles for a multiple QTL model | plotLodProfile |
| Plot genetic map | plot.map plotMap |
| Plot grid of missing genotypes | plotMissing |
| Plot a QTL model | plotModel |
| Plot a phenotype distribution | plotPheno |
| Plot phenotypes versus marker genotypes | plotPXG |
| Plot recombination fractions | plotRF |
| Pull out the results of the Viterbi algorithm from a cross | pull.argmaxgeno |
| Pull out the genotype imputations from a cross | pull.draws |
| Pull out the genotype data from a cross | pull.geno |
| Pull out the genotype probabilities from a cross | pull.genoprob |
| Pull out the genetic map from a cross | pull.map |
| Drop all but a selected set of markers | pull.markers |
| Pull out phenotype data from a cross | pull.pheno |
| Pull out recombination fractions or LOD scores from a cross object | pull.rf |
| Installed version of R/qtl | qtlversion |
| Read data for a QTL experiment | read.cross |
| Read data for 4- or 8-way RIL | readMWril |
| Reduce to a grid of pseudomarkers. | reduce2grid |
| Refine the positions of QTL | refineqtl |
| Reorder the QTL in a qtl object | reorderqtl |
| Replace the genetic map of a cross | replace.map replacemap.cross |
| Replace the genetic map in QTL mapping results with an alternate map | replacemap.scanone |
| Replace the genetic map in QTL mapping results with an alternate map | replacemap.scantwo |
| Replace a QTL in a qtl object with a different position | replaceqtl |
| Rescale genetic maps | rescalemap |
| Compare marker orders | ripple |
| Genome scan with a single QTL model | scanone |
| Bootstrap to get interval estimate of QTL location | scanoneboot |
| Genome scan for QTL affecting mean and/or variance | scanonevar |
| Permutation test for mean effect in scanonevar | scanonevar.meanperm |
| Permutation test for variance effect in scanonevar | scanonevar.varperm |
| Single-QTL genome scan to map QTL to a phylogenetic tree | scanPhyloQTL |
| General QTL scan | scanqtl |
| Two-dimensional genome scan with a two-QTL model | scantwo |
| Permutation test for 2d genome scan by Haley-Knott regression | scantwopermhk |
| Shift starting points in genetic maps | shiftmap |
| Simulate a QTL experiment | sim.cross |
| Simulate genotypes given observed marker data | sim.geno |
| Simulate a genetic map | sim.map |
| Simulate founder SNPs for a multiple-strain RIL | simFounderSnps |
| Simulate a set of intercrosses for a single diallelic QTL | simPhyloQTL |
| Simulates missing genotype data | simulatemissingdata |
| Stepwise selection for multiple QTL | stepwiseqtl |
| Strip partially informative genotypes | strip.partials |
| Subsetting data for QTL experiment | subset.cross [.cross |
| Subsetting chromosomes for a genetic map | subset.map [.map |
| Subsetting the results of a genome scan | subset.scanone |
| Subsetting permutation test results | subset.scanoneperm [.scanoneperm |
| Subsetting the results of a 2-d genome scan | subset.scantwo |
| Subsetting two-dimensional permutation test results | subset.scantwoperm [.scantwoperm |
| Print pairs of individuals with similar genotype data. | summary.comparegeno |
| Print summary of QTL experiment | summary.cross |
| Summary of fit of qtl model | summary.fitqtl |
| Print summary of a QTL object | summary.qtl |
| Print summary of ripple results | summary.ripple |
| Summarize the results of a genome scans | summary.scanone |
| Bootstrap confidence interval for QTL location | summary.scanoneboot |
| LOD thresholds from scanone permutation results | summary.scanoneperm |
| Summarize the results a genome scan to map a QTL to a phylogenetic tree | summary.scanPhyloQTL |
| Summarize the results of a two-dimensional genome scan | summary.scantwo |
| LOD thresholds from scantwo permutation results | summary.scantwoperm |
| Print summary of a genetic map | summary.map summaryMap |
| Summarize the results of a two-dimensional genome scan | summaryScantwoOld |
| Switch the order of markers on a chromosome | switch.order |
| Switch alleles at selected markers | switchAlleles |
| Convert a table of marker positions to a map object. | table2map |
| List genotypes with large error LOD scores | top.errorlod |
| Determine the total number of markers | totmar |
| Transformation of the phenotypes in a cross object | transformPheno |
| Test all possible positions for a marker | tryallpositions |
| Maximum distance between genotyped markers | typingGap |
| Write data for a QTL experiment to a file | write.cross |
| Get x-axis locations in scanone plot | xaxisloc.scanone |
