+.scanone               Arithmetic Operators for scanone and scantwo
                        results
+.scanoneperm           Arithmetic Operators for permutation results
A starting point        Introductory comments
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.scantwoperm           Combine data from scantwo permutations
calc.errorlod           Identify likely genotyping errors
calc.genoprob           Calculate conditional genotype probabilities
cbind.scanoneperm       Combine columns from multiple scanone
                        permutation results
checkAlleles            Identify markers with switched alleles
chrlen                  Chromosome lengths in QTL experiment
clean.cross             Remove derived data
clean.scantwo           Clean up scantwo output
comparecrosses          Compare two cross objects.
comparegeno             Compare individuals' genotype data
condense.scantwo        Condense the output from a 2-d genome scan
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
drop.markers            Drop a set of markers
drop.nullmarkers        Drop markers without any genotype data
effectplot              Plot phenotype means against genotypes at one
                        or two markers.
effectscan              Plot allelic effect 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.pheno              Find column number for a particular phenotype.
find.pseudomarker       Find the pseudomarker closest to a specified
                        position
fitqtl                  Fit a multiple-QTL model
fitstahl                Fit Stahl interference model
geno.table              Create table of genotype distributions
hyper                   Data on hypertension
jittermap               Jitter marker positions in a genetic map
listeria                Data on Listeria monocytogenes susceptibility
lodint                  LOD support interval
makeqtl                 Make a qtl object
map10                   An example genetic map
max.scanone             Maximum peak in genome scan
max.scantwo             Maximum peak in two-dimensional genome scan
movemarker              Move a marker to a new chromosome
nmissing                Number of missing genotypes
plot.cross              Plot various features of a cross object
plot.errorlod           Plot grid of error LOD values
plot.geno               Plot observed genotypes, flagging likely errors
plot.info               Plot the proportion of missing genotype
                        information
plot.map                Plot genetic map
plot.missing            Plot grid of missing genotypes
plot.pheno              Plot a phenotype distribution
plot.pxg                Plot phenotypes versus marker genotypes.
plot.rf                 Plot recombination fractions
plot.scanone            Plot LOD curves
plot.scantwo            Plot LOD scores for a two-dimensional genome
                        scan
pull.geno               Pull out the genotype data from a cross
pull.map                Pull out the genetic map from a cross
qtlversion              Installed version of R/qtl
read.cross              Read data for a QTL experiment
replace.map             Replace the genetic map of a cross
ripple                  Compare marker orders
scanone                 Genome scan with a single QTL model
scanqtl                 General QTL scan
scantwo                 Two-dimensional genome scan with a two-QTL
                        model
sim.cross               Simulate a QTL experiment
sim.geno                Simulate genotypes given observed marker data
sim.map                 Simulate a genetic map
strip.partials          Strip partially informative genotypes
subset.cross            Subsetting data for QTL experiment
subset.scanone          Subsetting the results of a genome scan
subset.scantwo          Subsetting the results of a 2-d genome scan
summary.cross           Print summary of QTL experiment
summary.fitqtl          Summary of fit of qtl model
summary.map             Print summary of a genetic map
summary.ripple          Print summary of ripple results
summary.scanone         Summarize the results of a genome scans
summary.scanoneperm     LOD thresholds from scanone permutation results
summary.scantwo         Summarize the results of a two-dimensional
                        genome scan
summary.scantwo.old     Summarize the results of a two-dimensional
                        genome scan
summary.scantwoperm     LOD thresholds from scantwo permutation results
switch.order            Switch the order of markers on a chromosome
top.errorlod            List genotypes with large error LOD scores
write.cross             Write data for a QTL experiment to a file
