A starting point         Introductory comments
argmax.geno              Reconstruct underlying genotypes
badorder                 An intercross with misplaced markers
c.cross                  Combine data for QTL experiments
calc.errorlod            Identify likely genotyping errors
calc.genoprob            Calculate conditional genotype probabilities
clean                    Remove derived data
convert2ss               Convert an intercross into a form to allow sex-
                         specific maps
drop.markers             Drop a set of markers
drop.nullmarkers         Drop markers without any genotype data
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
geno.table               Create table of genotype distributions
hyper                    Data on hypertension
listeria                 Data on Listeria monocytogenes susceptibility
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.rf                  Plot recombination fractions
plot.scanone             Plot LOD curves
plot.scantwo             Plot LOD scores for a two-dimensional genome
                         scan
pull.map                 Pull out the genetic map from a cross
qtl-internal             Internal qtl functions
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
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
subset.cross             Subsetting data for QTL experiment
summary.cross            Print summary of QTL experiment
summary.ripple           Print summary of ripple results
summary.scanone          Summarize the results of a genome scan
summary.scantwo          Summarize the results of a two-dimensional
                         genome scan
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
