+.scanone Arithmetic operators for scanone and scantwo
results
+.scanoneperm Arithmetic Operators for permutation results
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
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
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
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
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
convert2sa Convert a sex-specific map to a sex-averaged
one.
countXO Count number of obligate crossovers for each
individual
drop.markers Drop a set of markers
drop.nullmarkers Drop markers without any genotype data
dropfromqtl Drop a QTL from a qtl object
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.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
formLinkageGroups Partition markers into linkage groups
geno.crosstab Create table of two-locus genotypes
geno.image Plot grid of genotype data
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
locateXO Estimate locations of crossovers
lodint LOD support interval
makeqtl Make a qtl object
map10 An example genetic map
markernames Pull out the marker names from a cross
max.scanone Maximum peak in genome scan
max.scantwo Maximum peak in two-dimensional genome scan
movemarker Move a marker to a new chromosome
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
ntyped Number of genotypes
orderMarkers Find an initial order for markers within
chromosomes
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.qtl Plot QTL locations
plot.rf Plot recombination fractions
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
plotLodProfile Plot 1-d LOD profiles for a multiple QTL model
plotModel Plot a QTL model
pull.geno Pull out the genotype data from a cross
pull.map Pull out the genetic map from a cross
pull.pheno Pull out phenotype data from a cross
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
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.
ripple Compare marker orders
scanone Genome scan with a single QTL model
scanoneboot Bootstrap to get interval estimate of QTL
location
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
simFounderSnps Simulate founder SNPs for a multiple-strain RIL
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.map Print summary of a genetic map
summary.qtl Print summary of a QTL object
summary.ripple Print summary of ripple results
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.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
totmar Determine the total number of markers
tryallpositions Test all possible positions for a marker
write.cross Write data for a QTL experiment to a file
xaxisloc.scanone Get x-axis locations in scanone plot.
