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qtl (version 0.97-21)
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
2,669
Version
0.97-21
License
GPL version 2 or later
Maintainer
Karl W Broman Saunak Sen ssenjaxorg
Last Published
August 22nd, 2024
Functions in qtl (0.97-21)
Search all functions
argmax.geno
Reconstruct underlying genotypes
calc.errorlod
Identify likely genotyping errors
comparecrosses
Compare two cross objects.
plot.map
Plot genetic map
c.cross
Combine data for QTL experiments
plot.info
Plot the proportion of missing genotype information
plot.scantwo
Plot LOD scores for a two-dimensional genome scan
plot.missing
Plot grid of missing genotypes
lodint
LOD support interval
plot.cross
Plot various features of a cross object
top.errorlod
List genotypes with large error LOD scores
plot.pxg
Plot phenotypes versus marker genotypes.
geno.table
Create table of genotype distributions
plot.geno
Plot observed genotypes, flagging likely errors
drop.markers
Drop a set of markers
summary.ripple
Print summary of ripple results
scanqtl
General QTL scan
summary.cross
Print summary of QTL experiment
replace.map
Replace the genetic map of a cross
scantwo
Two-dimensional genome scan with a two-QTL model
fill.geno
Fill holes in genotype data
summary.scanone
Summarize the results of a genome scan
convert2ss
Convert an intercross into a form to allow sex-specific maps
find.marker
Find marker closest to a specified position
plot.errorlod
Plot grid of error LOD values
max.scantwo
Maximum peak in two-dimensional genome scan
plot.scanone
Plot LOD curves
pull.geno
Pull out the genotype data from a cross
scanone
Genome scan with a single QTL model
clean
Remove derived data
summary.fitqtl
Summary of fit of qtl model
est.rf
Estimate pairwise recombination fractions
summary.scantwo
Summarize the results of a two-dimensional genome scan
switch.order
Switch the order of markers on a chromosome
effectscan
Plot allelic effect across the whole genome
qtl-internal
Internal qtl functions
pull.map
Pull out the genetic map from a cross
nmissing
Number of missing genotypes
subset.cross
Subsetting data for QTL experiment
max.scanone
Maximum peak in genome scan
sim.map
Simulate a genetic map
plot.rf
Plot recombination fractions
A starting point
Introductory comments
write.cross
Write data for a QTL experiment to a file
sim.geno
Simulate genotypes given observed marker data
ripple
Compare marker orders
est.map
Estimate genetic maps
fitqtl
Fit a multiple QTL model
read.cross
Read data for a QTL experiment
sim.cross
Simulate a QTL experiment
drop.nullmarkers
Drop markers without any genotype data
calc.genoprob
Calculate conditional genotype probabilities
makeqtl
Make a qtl object
effectplot
Plot phenotype means against genotypes at one or two markers.
bristle3
Data on bristle number in Drosophila
map10
An example genetic map
fake.f2
Simulated data for an F2 intercross
bristleX
Data on bristle number in Drosophila
fake.bc
Simulated data for a backcross
listeria
Data on Listeria monocytogenes susceptibility
hyper
Data on hypertension
badorder
An intercross with misplaced markers
fake.4way
Simulated data for a 4-way cross