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qtl (version 0.92-3)
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
3,063
Version
0.92-3
License
GPL version 2 or later
Maintainer
Karl W Broman Saunak Sen ssenjaxorg
Last Published
August 22nd, 2024
Functions in qtl (0.92-3)
Search all functions
plot.rf
Plot recombination fractions
plot.missing
Plot grid of missing genotypes
calc.genoprob
Calculate conditional genotype probabilities
argmax.geno
Reconstruct underlying genotypes
ripple
Compare marker orders
summary.ripple
Print summary of ripple results
plot.map
Plot genetic map
drop.nullmarkers
Drop markers without any genotype data
plot.info
Plot the proportion of missing genotype information
summary.cross
Print summary of QTL experiment
c.cross
Combine data for QTL experiments
scanone
Genome scan with a single QTL model
subset.cross
Subsetting data for QTL experiment
write.cross
Write data for a QTL experiment to a file
clean
Remove derived data
drop.markers
Drop a set of markers
calc.errorlod
Identify likely genotyping errors
summary.scantwo
Summarize the results of a two-dimensional genome scan
plot.scantwo
Plot LOD scores for a two-dimensional genome scan
A starting point
Introductory comments
plot.geno
Plot observed genotypes, flagging likely errors
sim.map
Simulate a genetic map
plot.cross
Plot various features of a cross object
plot.scanone
Plot LOD curves
convert2ss
Convert an intercross into a form to allow sex-specific maps
replace.map
Replace the genetic map of a cross
est.rf
Estimate pairwise recombination fractions
sim.geno
Simulate genotypes given observed marker data
read.cross
Read data for a QTL experiment
plot.errorlod
Plot grid of error LOD values
pull.map
Pull out the genetic map from a cross
geno.table
Create table of genotype distributions
summary.scanone
Summarize the results of a genome scan
scantwo
Two-dimensional genome scan with a two-QTL model
top.errorlod
List genotypes with large error LOD scores
sim.cross
Simulate a QTL experiment
est.map
Estimate genetic maps
qtl-internal
Internal qtl functions
switch.order
Switch the order of markers on a chromosome
fill.geno
Fill holes in genotype data
fake.4way
Simulated data for a 4-way cross
hyper
Data on hypertension
listeria
Data on Listeria monocytogenes susceptibility
fake.f2
Simulated data for an F2 intercross
badorder
An intercross with misplaced markers
fake.bc
Simulated data for a backcross