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qtl (version 0.99-22)

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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Version

Install

install.packages('qtl')

Monthly Downloads

2,669

Version

0.99-22

License

GPL version 2 or later

Maintainer

Karl W Broman Saunak Sen ssenjaxorg

Last Published

August 22nd, 2024

Functions in qtl (0.99-22)

find.flanking

Find flanking markers for a specified position
clean

Remove derived data
plot.scantwo

Plot LOD scores for a two-dimensional genome scan
find.marker

Find marker closest to a specified position
summary.fitqtl

Summary of fit of qtl model
plot.info

Plot the proportion of missing genotype information
geno.table

Create table of genotype distributions
est.rf

Estimate pairwise recombination fractions
read.cross

Read data for a QTL experiment
c.cross

Combine data for QTL experiments
lodint

LOD support interval
convert2ss

Convert an intercross into a form to allow sex-specific maps
sim.map

Simulate a genetic map
plot.scanone

Plot LOD curves
makeqtl

Make a qtl object
max.scanone

Maximum peak in genome scan
plot.geno

Plot observed genotypes, flagging likely errors
replace.map

Replace the genetic map of a cross
plot.missing

Plot grid of missing genotypes
scantwo

Two-dimensional genome scan with a two-QTL model
summary.ripple

Print summary of ripple results
ripple

Compare marker orders
plot.cross

Plot various features of a cross object
effectplot

Plot phenotype means against genotypes at one or two markers.
summary.map

Print summary of a genetic map
pull.map

Pull out the genetic map from a cross
plot.map

Plot genetic map
summary.scanone

Summarize the results of one or several one-QTL genome scans
comparegeno

Compare individuals' genotype data
arithscan

Arithmetic Operators for genome scan results
est.map

Estimate genetic maps
pull.geno

Pull out the genotype data from a cross
calc.genoprob

Calculate conditional genotype probabilities
scanqtl

General QTL scan
effectscan

Plot allelic effect across the whole genome
strip.partials

Strip partially informative genotypes
fill.geno

Fill holes in genotype data
sim.geno

Simulate genotypes given observed marker data
summary.scantwo

Summarize the results of a two-dimensional genome scan
sim.cross

Simulate a QTL experiment
plot.rf

Plot recombination fractions
argmax.geno

Reconstruct underlying genotypes
comparecrosses

Compare two cross objects.
max.scantwo

Maximum peak in two-dimensional genome scan
A starting point

Introductory comments
find.pheno

Find column number for a particular phenotype.
subset.cross

Subsetting data for QTL experiment
summary.cross

Print summary of QTL experiment
plot.errorlod

Plot grid of error LOD values
nmissing

Number of missing genotypes
qtl-internal

Internal qtl functions
print.cross

Print a QTL experiment
scanone

Genome scan with a single QTL model
switch.order

Switch the order of markers on a chromosome
plot.pxg

Plot phenotypes versus marker genotypes.
calc.errorlod

Identify likely genotyping errors
drop.markers

Drop a set of markers
movemarker

Move a marker to a new chromosome
convert.scanone

Convert output from scanone for R/qtl version 0.98
fitqtl

Fit a multiple QTL model
top.errorlod

List genotypes with large error LOD scores
bayesint

Bayesian probability interval
drop.nullmarkers

Drop markers without any genotype data
write.cross

Write data for a QTL experiment to a file
fake.f2

Simulated data for an F2 intercross
badorder

An intercross with misplaced markers
fake.4way

Simulated data for a 4-way cross
bristleX

Data on bristle number in Drosophila
map10

An example genetic map
hyper

Data on hypertension
listeria

Data on Listeria monocytogenes susceptibility
fake.bc

Simulated data for a backcross
bristle3

Data on bristle number in Drosophila