Rdocumentation
powered by
Learn R Programming
⚠️
There's a newer version (1.74) of this package.
Take me there.
qtl (version 0.85-4)
Tools for analyzing QTL experiments
Description
Analysis of experimental crosses to identify QTLs
Copy Link
Link to current version
Version
Version
1.74
1.72
1.70
1.66
1.62
1.60
1.58
1.54
1.52
1.50
1.48-1
1.47-9
1.46-2
1.45-11
1.44-9
1.42-8
1.41-6
1.40-8
1.39-5
1.38-4
1.37-11
1.36-6
1.35-3
1.35-1
1.34-17
1.34-16
1.33-7
1.32-10
1.31-9
1.30-4
1.29-2
1.28-19
1.27-10
1.26-14
1.26-13
1.25-15
1.24-9
1.23-16
1.22-21
1.21-2
1.20-15
1.19-20
1.18-7
1.17-39
1.16-6
1.16-4
1.15-15
1.14-2
1.13-7
1.12-26
1.11-12
1.10-27
1.09-43
1.08-56
1.08-55
1.07-12
1.07-11
1.06-43
1.05-2
1.04-53
1.04-52
1.03-14
1.02-26
1.01-9
1.00-17
1.00-16
1.00-15
0.99-24
0.99-22
0.98-57
0.97-22
0.97-21
0.96-5
0.92-3
0.85-4
Install
install.packages('qtl')
Monthly Downloads
7,337
Version
0.85-4
License
GPL version 2 or newer
Maintainer
Karl W Broman Saunak Sen ssenjaxorg
Last Published
December 8th, 2025
Functions in qtl (0.85-4)
Search all functions
read.cross.csv
Read data for a QTL experiment in comma-delimited format
sim.map
Simulate a genetic map
drop.nullmarkers
Drop markers without any genotype data
est.map
Estimate genetic maps
plot.cross
Plot various features of a cross object
plot.missing
Plot grid of missing genotypes
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
vbscan.perm
Permutation test for trait with some undefined values
plot.map
Plot genetic map
write.cross.mm
Write data in mapmaker format
pull.chr
Pull out a subset of chromosomes from a cross
plot.info
Plot the proportion of missing information in the genotype data
clean
Remove intermediate calculations
sim.geno
Simulate genotypes given observed marker data
plot.geno
Plot genotypes with indication of likely errors
drop.markers
Drop a set of markers
drop.qtlgeno
Remove QTL genotypes
ripple
Compare marker orders
write.cross.csv
Write data in comma-delimited format
vbscan
Genome scan for trait with some undefined values
top.errorlod
List genotypes with highest error LOD values
convert2ss
Convert an intercross into a form to allow sex-specific maps
est.rf
Estimate pairwise recombination fractions
sim.cross
Simulate a QTL experiment
plot.errors
Plot grid of likely genotyping errors
argmax.geno
Reconstruct underlying genotypes
summary.ripple
Print summary of ripple results
plot.rf
Plot recombination fractions
summary.scanone
Print summary of the scanone output
plot.errorlod
Plot grid of error LOD values
scanone.perm
Permutation test for genome scan with single QTL model
geno.table
Create table of genotype distributions
calc.errorlod
Identify likely genotyping errors
read.cross.mm
Read data for a QTL experiment in mapmaker format
replace.map
Replace the genetic map of a cross
A starting point
Introductory comments
find.errors
Identify likely genotyping errors
switch.order
Switch the order of markers on a chromosome
write.cross
Write data for a QTL experiment to a file
scanone
Genome scan with single QTL model
calc.genoprob
Calculate conditional genotype probabilities
pull.map
Pull out the genetic map from a cross
summary.cross
Print summary of QTL experiment
plot.scanone
Plot output for a single QTL scan
read.cross
Read data for a QTL experiment
fake.bc
Simulated data for a backcross experiment
fake.f2
Simulated data for an F2 intercross experiment
listeria
Data on Listeria monocytogenes susceptibility
hyper
Data on hypertension
fake.4way
Simulated data for a 4-way cross experiment