Tools for analyzing QTL experiments

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Documentation for package `qtl' version 0.98-57

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-- A --

A starting point Introductory comments
argmax.geno Reconstruct underlying genotypes

-- B --

badorder An intercross with misplaced markers
bristle3 Data on bristle number in Drosophila
bristleX Data on bristle number in Drosophila

-- C --

c.cross Combine data for QTL experiments
calc.errorlod Identify likely genotyping errors
calc.genoprob Calculate conditional genotype probabilities
clean Remove derived data
comparecrosses Compare two cross objects.
convert.scanone Convert output from scanone for R/qtl version 0.98
convert2ss Convert an intercross into a form to allow sex-specific maps

-- D --

drop.markers Drop a set of markers
drop.nullmarkers Drop markers without any genotype data

-- E --

effectplot Plot phenotype means against genotypes at one or two markers.
effectscan Plot allelic effect across the whole genome Estimate genetic maps
est.rf Estimate pairwise recombination fractions

-- F --

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.
fitqtl Fit a multiple QTL model

-- G --

geno.table Create table of genotype distributions

-- H --

hyper Data on hypertension

-- L --

listeria Data on Listeria monocytogenes susceptibility
lodint LOD support interval

-- M --

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

-- N --

nchr Print summary of QTL experiment
nind Print summary of QTL experiment
nmar Print summary of QTL experiment
nmissing Number of missing genotypes
nphe Print summary of QTL experiment

-- P --

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 the proportion of missing genotype information Plot genetic map
plot.missing Plot grid of missing genotypes
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
print.cross Print a QTL experiment
pull.geno Pull out the genotype data from a cross Pull out the genetic map from a cross

-- R --

read.cross Read data for a QTL experiment Replace the genetic map of a cross
ripple Compare marker orders

-- S --

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 Simulate a genetic map
subset.cross Subsetting data for QTL experiment
summary.cross Print summary of QTL experiment
summary.fitqtl Summary of fit of qtl model Print summary of a genetic map
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

-- T --

top.errorlod List genotypes with large error LOD scores
totmar Print summary of QTL experiment

-- W --

write.cross Write data for a QTL experiment to a file