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