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R/qtl: A QTL mapping environment

Authors: Karl W Broman and Hao Wu, with ideas from Gary Churchill and Śaunak Sen and contributions from Danny Arends, Robert Corty, Timothée Flutre, Ritsert Jansen, Pjotr Prins, Lars Rönnegård, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell

R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses. It is implemented as an add-on package for the freely available and widely used statistical language/software R. The development of this software as an add-on to R allows us to take advantage of the basic mathematical and statistical functions, and powerful graphics capabilities, that are provided with R. Further, the user will benefit by the seamless integration of the QTL mapping software into a general statistical analysis program. Our goal is to make complex QTL mapping methods widely accessible and allow users to focus on modeling rather than computing.

A key component of computational methods for QTL mapping is the hidden Markov model (HMM) technology for dealing with missing genotype data. We have implemented the main HMM algorithms, with allowance for the presence of genotyping errors, for backcrosses, intercrosses, and phase-known four-way crosses.

The current version of R/qtl includes facilities for estimating genetic maps, identifying genotyping errors, and performing single-QTL genome scans and two-QTL, two-dimensional genome scans, by interval mapping (with the EM algorithm), Haley-Knott regression, and multiple imputation. All of this may be done in the presence of covariates (such as sex, age or treatment). One may also fit higher-order QTL models by multiple imputation and Haley-Knott regression.

License

The R/qtl package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3

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Install

install.packages('qtl')

Monthly Downloads

2,669

Version

1.46-2

License

GPL-3

Issues

5

Pull Requests

0

Stars

84

Forks

46

Maintainer

Karl Broman

Last Published

March 11th, 2020

Functions in qtl (1.46-2)

addint

Add pairwise interaction to a multiple-QTL model
addcovarint

Add QTL x covariate interaction to a multiple-QTL model
addqtl

Scan for an additional QTL in a multiple-QTL model
addloctocross

Add phenotype location into a cross object
argmax.geno

Reconstruct underlying genotypes
add.threshold

Add significance threshold to plot
addtoqtl

Add to a qtl object
arithscanperm

Arithmetic Operators for permutation results
bayesint

Bayesian credible interval
MQM

Introduction to Multiple QTL Model (MQM) mapping
A starting point

Introductory comments on R/qtl
addmarker

Add a marker to a cross
addpair

Scan for an additional pair of QTL in a multiple-QTL model
add.cim.covar

Indicate marker covariates from composite interval mapping
allchrsplits

Test all possible splits of a chromosome into two pieces
badorder

An intercross with misplaced markers
calc.penalties

Calculate LOD penalties
calc.genoprob

Calculate conditional genotype probabilities
c.cross

Combine data for QTL experiments
drop.markers

Drop a set of markers
bristle3

Data on bristle number in Drosophila
comparecrosses

Compare two cross objects
calc.errorlod

Identify likely genotyping errors
bristleX

Data on bristle number in Drosophila
cbind.scantwoperm

Combine scantwo permutations by column
cbind.scanoneperm

Combine columns from multiple scanone permutation results
condense.scantwo

Condense the output from a 2-d genome scan
compareorder

Compare two orderings of markers on a chromosome
c.scantwoperm

Combine data from scantwo permutations
find.markerpos

Find position of a marker
est.map

Estimate genetic maps
clean.scantwo

Clean up scantwo output
est.rf

Estimate pairwise recombination fractions
drop.nullmarkers

Drop markers without any genotype data
c.scantwo

Combine columns from multiple scantwo results
convert.scanone

Convert output from scanone for R/qtl version 0.98
fake.f2

Simulated data for an F2 intercross
convert.scantwo

Convert output from scantwo for R/qtl version 1.03 and earlier
cleanGeno

Delete genotypes that are possibly in error
find.pheno

Find column number for a particular phenotype
checkAlleles

Identify markers with switched alleles
comparegeno

Compare individuals' genotype data
arithscan

Arithmetic operators for scanone and scantwo results
chrlen

Chromosome lengths in QTL experiment
convert2riself

Convert a cross to RIL by selfing
c.scanone

Combine columns from multiple scanone results
inferFounderHap

Crude reconstruction of founder haplotypes in multi-parent RIL
inferredpartitions

Identify inferred partitions in mapping QTL to a phylogenetic tree
convert.map

Change map function for a genetic map
map2table

Convert genetic map from list to table.
chrnames

Pull out the chromosome names from a cross
mapthis

Simulated data for illustrating genetic map construction
convert2risib

Convert a cross to RIL by sib mating
dropfromqtl

Drop a QTL from a qtl object
droponemarker

Drop one marker at a time and determine effect on genetic map
c.scanoneperm

Combine data from scanone permutations
convert2sa

Convert a sex-specific map to a sex-averaged one
effectscan

Plot estimated QTL effects across the whole genome
fitqtl

Fit a multiple-QTL model
cim

Composite interval mapping
effectplot

Plot phenotype means against genotypes at one or two markers
fill.geno

Fill holes in genotype data
find.markerindex

Determine the numeric index for a marker
find.flanking

Find flanking markers for a specified position
geno.image

Plot grid of genotype data
geno.crosstab

Create table of two-locus genotypes
find.marker

Find marker closest to a specified position
lodint

LOD support interval
formMarkerCovar

Create matrix of marker covariates for QTL analysis
formLinkageGroups

Partition markers into linkage groups
locations

Genetic locations of traits for the multitrait dataset
fitstahl

Fit Stahl interference model
makeqtl

Make a qtl object
flip.order

Flip the orders of markers on a set of chromosomes
max.scanPhyloQTL

Maximum peak in genome scan to map a QTL to a phylogenetic tree
mqmplot.clusteredheatmap

Plot clustered heatmap of MQM scan on multiple phenotypes
interpPositions

Interpolate positions from one map to another
geno.table

Create table of genotype distributions
max.scanone

Maximum peak in genome scan
getid

Pull out the individual identifiers from a cross
max.scantwo

Maximum peak in two-dimensional genome scan
movemarker

Move a marker to a new chromosome
jittermap

Jitter marker positions in a genetic map
clean.cross

Remove derived data
map10

An example genetic map
fake.bc

Simulated data for a backcross
drop.dupmarkers

Drop duplicate markers
fake.4way

Simulated data for a 4-way cross
countXO

Count number of obligate crossovers for each individual
mqmextractmarkers

MQM marker extraction
mqmplot.multitrait

Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes
mqmplot.permutations

Plot results from mqmpermutation
mqmfind.marker

Fetch significant markers after permutation analysis
nqtl

Determine the number of QTL in a QTL object
mqmplot.cofactors

Plot cofactors on the genetic map
mqmplot.singletrait

Plot LOD curves of a multiple-QTL model
mqmtestnormal

Shapiro normality test used for MQM
multitrait

Example Cross object from R/QTL with multiple traits
nphe

Determine the number of phenotypes QTL experiment
mqmprocesspermutation

Convert mqmmulti objects into a scanoneperm object
plotInfo

Plot the proportion of missing genotype information
find.pseudomarker

Find the pseudomarker closest to a specified position
findDupMarkers

Find markers with identical genotype data
ntyped

Number of genotypes
plot.comparegeno

Plot genotype comparison
nqrank

Transform a vector of quantitative values to the corresponding normal quantiles
mqmgetmodel

Retrieve the QTL model used in mapping from the results of an MQM scan
groupclusteredheatmap

Retrieving groups of traits after clustering
hyper

Data on hypertension
plotMap

Plot genetic map
listeria

Data on Listeria monocytogenes susceptibility
mqmaugment

MQM augmentation
mqmplot.circle

Circular genome plot for MQM
mqmscanfdr

Estimate FDR for multiple trait QTL analysis
plot.cross

Plot various features of a cross object
plotLodProfile

Plot 1-d LOD profiles for a multiple QTL model
mqmautocofactors

Automatic setting of cofactors, taking marker density into account
mqmsetcofactors

Set cofactors at fixed intervals, to be used with MQM
phenames

Pull out the phenotypes names from a cross
mqmpermutation

Estimate QTL LOD score significance using permutations or simulations
pickMarkerSubset

Identify the largest subset of markers that are some distance apart
plotModel

Plot a QTL model
pull.pheno

Pull out phenotype data from a cross
markerlrt

General likelihood ratio test for association between marker pairs
mqmplot.cistrans

cis-trans plot
plot.scanoneperm

Plot permutation results for a single-QTL genome scan
plot.scanoneboot

Plot results of bootstrap for QTL position
mqmplot.directedqtl

Plot LOD*Effect curves of a multiple-QTL model
mqmscan

Genome scan with a multiple QTL model (MQM)
qtlversion

Installed version of R/qtl
pull.rf

Pull out recombination fractions or LOD scores from a cross object
locateXO

Estimate locations of crossovers
mqmscanall

Parallelized MQM on multiple phenotypes in a cross object
plotErrorlod

Plot grid of error LOD values
qtl-internal

Internal qtl functions
reduce2grid

Reduce to a grid of pseudomarkers.
markernames

Pull out the marker names from a cross
nmar

Determine the numbers of markers on each chromosome
mqmplot.heatmap

Heatmap of a genome of MQM scan on multiple phenotypes
nchr

Determine the number of chromosomes
nind

Determine the number of individuals QTL experiment
rescalemap

Rescale genetic maps
replaceqtl

Replace a QTL in a qtl object with a different position
scanonevar.varperm

Permutation test for variance effect in scanonevar
plotPXG

Plot phenotypes versus marker genotypes
orderMarkers

Find an initial order for markers within chromosomes
nullmarkers

Identify markers without any genotype data
scanqtl

General QTL scan
nmissing

Number of missing genotypes
plot.qtl

Plot QTL locations
refineqtl

Refine the positions of QTL
plotRF

Plot recombination fractions
plotGeno

Plot observed genotypes, flagging likely errors
plot.scantwo

Plot LOD scores for a two-dimensional genome scan
scanone

Genome scan with a single QTL model
subset.scantwoperm

Subsetting two-dimensional permutation test results
sim.cross

Simulate a QTL experiment
subset.map

Subsetting chromosomes for a genetic map
scanoneboot

Bootstrap to get interval estimate of QTL location
subset.scanone

Subsetting the results of a genome scan
plot.rfmatrix

Plot recombination fractions or LOD scores for a single marker
strip.partials

Strip partially informative genotypes
plotPheno

Plot a phenotype distribution
summary.comparegeno

Print pairs of individuals with similar genotype data.
plot.scantwoperm

Plot permutation results for a 2d, 2-QTL genome scan
pull.genoprob

Pull out the genotype probabilities from a cross
subset.cross

Subsetting data for QTL experiment
shiftmap

Shift starting points in genetic maps
plotMissing

Plot grid of missing genotypes
plot.scanPhyloQTL

Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree
readMWril

Read data for 4- or 8-way RIL
pull.draws

Pull out the genotype imputations from a cross
pull.map

Pull out the genetic map from a cross
pull.argmaxgeno

Pull out the results of the Viterbi algorithm from a cross
plot.scanone

Plot LOD curves
pull.geno

Pull out the genotype data from a cross
scantwo

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

Read data for a QTL experiment
pull.markers

Drop all but a selected set of markers
replacemap.scantwo

Replace the genetic map in QTL mapping results with an alternate map
scanonevar.meanperm

Permutation test for mean effect in scanonevar
replacemap.scanone

Replace the genetic map in QTL mapping results with an alternate map
ripple

Compare marker orders
scantwopermhk

Permutation test for 2d genome scan by Haley-Knott regression
sim.geno

Simulate genotypes given observed marker data
summary.cross

Print summary of QTL experiment
scanPhyloQTL

Single-QTL genome scan to map QTL to a phylogenetic tree
sim.map

Simulate a genetic map
summary.scanoneboot

Bootstrap confidence interval for QTL location
reorderqtl

Reorder the QTL in a qtl object
summary.scanone

Summarize the results of a genome scans
simulatemissingdata

Simulates missing genotype data
subset.scantwo

Subsetting the results of a 2-d genome scan
subset.scanoneperm

Subsetting permutation test results
scanonevar

Genome scan for QTL affecting mean and/or variance
stepwiseqtl

Stepwise selection for multiple QTL
replace.map

Replace the genetic map of a cross
summary.scanoneperm

LOD thresholds from scanone permutation results
simFounderSnps

Simulate founder SNPs for a multiple-strain RIL
summary.fitqtl

Summary of fit of qtl model
switch.order

Switch the order of markers on a chromosome
summaryMap

Print summary of a genetic map
summary.qtl

Print summary of a QTL object
switchAlleles

Switch alleles at selected markers
summary.scantwo

Summarize the results of a two-dimensional genome scan
totmar

Determine the total number of markers
summary.ripple

Print summary of ripple results
summary.scanPhyloQTL

Summarize the results a genome scan to map a QTL to a phylogenetic tree
simPhyloQTL

Simulate a set of intercrosses for a single diallelic QTL
typingGap

Maximum distance between genotyped markers
transformPheno

Transformation of the phenotypes in a cross object
tryallpositions

Test all possible positions for a marker
summaryScantwoOld

Summarize the results of a two-dimensional genome scan
summary.scantwoperm

LOD thresholds from scantwo permutation results
top.errorlod

List genotypes with large error LOD scores
table2map

Convert a table of marker positions to a map object.
write.cross

Write data for a QTL experiment to a file
xaxisloc.scanone

Get x-axis locations in scanone plot