A starting point         Introductory comments
argmax.geno              Reconstruct underlying genotypes
calc.errorlod            Identify likely genotyping errors
calc.genoprob            Calculate conditional genotype probabilities
clean                    Remove intermediate calculations
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
drop.qtlgeno             Remove QTL genotypes
est.map                  Estimate genetic maps
est.rf                   Estimate pairwise recombination fractions
fake.4way                Simulated data for a 4-way cross experiment
fake.bc                  Simulated data for a backcross experiment
fake.f2                  Simulated data for an F2 intercross experiment
find.errors              Identify likely genotyping errors
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.errors              Plot grid of likely genotyping errors
plot.geno                Plot genotypes with indication of likely errors
plot.info                Plot the proportion of missing information in
                         the genotype data
plot.map                 Plot genetic map
plot.missing             Plot grid of missing genotypes
plot.rf                  Plot recombination fractions
plot.scanone             Plot output for a single QTL scan
pull.chr                 Pull out a subset of chromosomes from a cross
pull.map                 Pull out the genetic map from a cross
read.cross               Read data for a QTL experiment
read.cross.csv           Read data for a QTL experiment in comma-
                         delimited format
read.cross.gary          Read data for a QTL experiment in Gary
                         Churchill's format
read.cross.karl          Read data for a QTL experiment in Karl Broman's
                         format
read.cross.mm            Read data for a QTL experiment in mapmaker
                         format
replace.map              Replace the genetic map of a cross
ripple                   Compare marker orders
scanone                  Genome scan with single QTL model
scanone.perm             Permutation test for genome scan with single QTL
                         model
sim.cross                Simulate a QTL experiment
sim.geno                 Simulate genotypes given observed marker data
sim.map                  Simulate a genetic map
summary.cross            Print summary of QTL experiment
summary.ripple           Print summary of ripple results
summary.scanone          Print summary of the scanone output
switch.order             Switch the order of markers on a chromosome
top.errorlod             List genotypes with highest error LOD values
vbscan                   Genome scan for trait with some undefined values
vbscan.perm              Permutation test for trait with some undefined
                         values
write.cross              Write data for a QTL experiment to a file
write.cross.csv          Write data in comma-delimited format
write.cross.mm           Write data in mapmaker format
