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qtl (version 0.97-22)
Tools for analyzing QTL experiments
Description
Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
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Install
install.packages('qtl')
Monthly Downloads
7,337
Version
0.97-22
License
GPL version 2 or later
Maintainer
Karl W Broman Saunak Sen ssenjaxorg
Last Published
December 8th, 2025
Functions in qtl (0.97-22)
Search all functions
drop.nullmarkers
Drop markers without any genotype data
makeqtl
Make a qtl object
A starting point
Introductory comments
argmax.geno
Reconstruct underlying genotypes
effectscan
Plot allelic effect across the whole genome
effectplot
Plot phenotype means against genotypes at one or two markers.
drop.markers
Drop a set of markers
summary.ripple
Print summary of ripple results
pull.map
Pull out the genetic map from a cross
sim.map
Simulate a genetic map
scanqtl
General QTL scan
summary.cross
Print summary of QTL experiment
plot.pxg
Plot phenotypes versus marker genotypes.
plot.info
Plot the proportion of missing genotype information
plot.cross
Plot various features of a cross object
c.cross
Combine data for QTL experiments
summary.fitqtl
Summary of fit of qtl model
summary.scanone
Summarize the results of a genome scan
qtl-internal
Internal qtl functions
sim.geno
Simulate genotypes given observed marker data
convert2ss
Convert an intercross into a form to allow sex-specific maps
lodint
LOD support interval
top.errorlod
List genotypes with large error LOD scores
geno.table
Create table of genotype distributions
find.marker
Find marker closest to a specified position
summary.scantwo
Summarize the results of a two-dimensional genome scan
plot.map
Plot genetic map
clean
Remove derived data
nmissing
Number of missing genotypes
subset.cross
Subsetting data for QTL experiment
replace.map
Replace the genetic map of a cross
fill.geno
Fill holes in genotype data
plot.scantwo
Plot LOD scores for a two-dimensional genome scan
write.cross
Write data for a QTL experiment to a file
pull.geno
Pull out the genotype data from a cross
switch.order
Switch the order of markers on a chromosome
ripple
Compare marker orders
plot.errorlod
Plot grid of error LOD values
fitqtl
Fit a multiple QTL model
calc.genoprob
Calculate conditional genotype probabilities
max.scantwo
Maximum peak in two-dimensional genome scan
read.cross
Read data for a QTL experiment
max.scanone
Maximum peak in genome scan
plot.missing
Plot grid of missing genotypes
sim.cross
Simulate a QTL experiment
plot.scanone
Plot LOD curves
comparecrosses
Compare two cross objects.
est.map
Estimate genetic maps
plot.geno
Plot observed genotypes, flagging likely errors
est.rf
Estimate pairwise recombination fractions
scantwo
Two-dimensional genome scan with a two-QTL model
scanone
Genome scan with a single QTL model
plot.rf
Plot recombination fractions
calc.errorlod
Identify likely genotyping errors
bristle3
Data on bristle number in Drosophila
badorder
An intercross with misplaced markers
listeria
Data on Listeria monocytogenes susceptibility
bristleX
Data on bristle number in Drosophila
fake.4way
Simulated data for a 4-way cross
fake.f2
Simulated data for an F2 intercross
map10
An example genetic map
hyper
Data on hypertension
fake.bc
Simulated data for a backcross