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qtl (version 1.01-9)

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

3,345

Version

1.01-9

License

GPL version 2 or later

Maintainer

Karl W Broman Saunak Sen ssenjaxorg

Last Published

August 22nd, 2024

Functions in qtl (1.01-9)

convert2ss

Convert an intercross into a form to allow sex-specific maps
plot.missing

Plot grid of missing genotypes
plot.pxg

Plot phenotypes versus marker genotypes.
geno.table

Create table of genotype distributions
sim.cross

Simulate a QTL experiment
qtl-internal

Internal qtl functions
ripple

Compare marker orders
plot.rf

Plot recombination fractions
effectscan

Plot allelic effect across the whole genome
pull.map

Pull out the genetic map from a cross
max.scantwo

Maximum peak in two-dimensional genome scan
plot.cross

Plot various features of a cross object
find.flanking

Find flanking markers for a specified position
top.errorlod

List genotypes with large error LOD scores
bayesint

Bayesian probability interval
plot.geno

Plot observed genotypes, flagging likely errors
fitqtl

Fit a multiple QTL model
effectplot

Plot phenotype means against genotypes at one or two markers.
plot.errorlod

Plot grid of error LOD values
fill.geno

Fill holes in genotype data
scantwo

Two-dimensional genome scan with a two-QTL model
write.cross

Write data for a QTL experiment to a file
drop.markers

Drop a set of markers
sim.geno

Simulate genotypes given observed marker data
argmax.geno

Reconstruct underlying genotypes
find.marker

Find marker closest to a specified position
qtlversion

Installed version of R/qtl
max.scanone

Maximum peak in genome scan
print.cross

Print a QTL experiment
pull.geno

Pull out the genotype data from a cross
scanone

Genome scan with a single QTL model
scanqtl

General QTL scan
strip.partials

Strip partially informative genotypes
calc.errorlod

Identify likely genotyping errors
est.map

Estimate genetic maps
arithscan

Arithmetic Operators for genome scan results
plot.scanone

Plot LOD curves
find.pheno

Find column number for a particular phenotype.
drop.nullmarkers

Drop markers without any genotype data
c.cross

Combine data for QTL experiments
plot.map

Plot genetic map
movemarker

Move a marker to a new chromosome
calc.genoprob

Calculate conditional genotype probabilities
A starting point

Introductory comments
sim.map

Simulate a genetic map
makeqtl

Make a qtl object
est.rf

Estimate pairwise recombination fractions
summary.cross

Print summary of QTL experiment
comparegeno

Compare individuals' genotype data
summary.map

Print summary of a genetic map
switch.order

Switch the order of markers on a chromosome
summary.fitqtl

Summary of fit of qtl model
summary.scanone

Summarize the results of one or several one-QTL genome scans
plot.scantwo

Plot LOD scores for a two-dimensional genome scan
comparecrosses

Compare two cross objects.
summary.ripple

Print summary of ripple results
replace.map

Replace the genetic map of a cross
summary.scantwo

Summarize the results of a two-dimensional genome scan
nmissing

Number of missing genotypes
clean

Remove derived data
lodint

LOD support interval
plot.info

Plot the proportion of missing genotype information
subset.cross

Subsetting data for QTL experiment
convert.scanone

Convert output from scanone for R/qtl version 0.98
read.cross

Read data for a QTL experiment
badorder

An intercross with misplaced markers
bristleX

Data on bristle number in Drosophila
map10

An example genetic map
fake.f2

Simulated data for an F2 intercross
bristle3

Data on bristle number in Drosophila
listeria

Data on Listeria monocytogenes susceptibility
hyper

Data on hypertension
fake.bc

Simulated data for a backcross
fake.4way

Simulated data for a 4-way cross