RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (1.66) of this package.
Take me there.
qtl (version 1.42-8)
Tools for Analyzing QTL Experiments
Description
Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
Copy Link
Copy
Link to current version
Version
Version
1.66
1.62
1.60
1.58
1.54
1.52
1.50
1.48-1
1.47-9
1.46-2
1.45-11
1.44-9
1.42-8
1.41-6
1.40-8
1.39-5
1.38-4
1.37-11
1.36-6
1.35-3
1.35-1
1.34-17
1.34-16
1.33-7
1.32-10
1.31-9
1.30-4
1.29-2
1.28-19
1.27-10
1.26-14
1.26-13
1.25-15
1.24-9
1.23-16
1.22-21
1.21-2
1.20-15
1.19-20
1.18-7
1.17-39
1.16-6
1.16-4
1.15-15
1.14-2
1.13-7
1.12-26
1.11-12
1.10-27
1.09-43
1.08-56
1.08-55
1.07-12
1.07-11
1.06-43
1.05-2
1.04-53
1.04-52
1.03-14
1.02-26
1.01-9
1.00-17
1.00-16
1.00-15
0.99-24
0.99-22
0.98-57
0.97-22
0.97-21
0.96-5
0.92-3
0.85-4
Down Chevron
Install
install.packages('qtl')
Monthly Downloads
3,873
Version
1.42-8
License
GPL-3
Issues
5
Pull Requests
0
Stars
77
Forks
45
Repository
https://github.com/kbroman/qtl
Homepage
https://rqtl.org
Maintainer
Karl W Broman
Last Published
February 19th, 2018
Functions in qtl (1.42-8)
Search functions
add.cim.covar
Indicate marker covariates from composite interval mapping
addloctocross
Add phenotype location into a cross object
addmarker
Add a marker to a cross
bristle3
Data on bristle number in Drosophila
arithscanperm
Arithmetic Operators for permutation results
calc.penalties
Calculate LOD penalties
c.cross
Combine data for QTL experiments
c.scantwo
Combine columns from multiple scantwo results
c.scantwoperm
Combine data from scantwo permutations
badorder
An intercross with misplaced markers
comparecrosses
Compare two cross objects
comparegeno
Compare individuals' genotype data
calc.errorlod
Identify likely genotyping errors
cbind.scanoneperm
Combine columns from multiple scanone permutation results
MQM
Introduction to Multiple QTL Model (MQM) mapping
drop.markers
Drop a set of markers
condense.scantwo
Condense the output from a 2-d genome scan
compareorder
Compare two orderings of markers on a chromosome
calc.genoprob
Calculate conditional genotype probabilities
convert.map
Change map function for a genetic map
chrlen
Chromosome lengths in QTL experiment
drop.nullmarkers
Drop markers without any genotype data
chrnames
Pull out the chromosome names from a cross
convert.scanone
Convert output from scanone for R/qtl version 0.98
A starting point
Introductory comments on R/qtl
effectplot
Plot phenotype means against genotypes at one or two markers
fake.f2
Simulated data for an F2 intercross
addtoqtl
Add to a qtl object
allchrsplits
Test all possible splits of a chromosome into two pieces
c.scanone
Combine columns from multiple scanone results
cleanGeno
Delete genotypes that are possibly in error
countXO
Count number of obligate crossovers for each individual
c.scanoneperm
Combine data from scanone permutations
drop.dupmarkers
Drop duplicate markers
clean.scantwo
Clean up scantwo output
find.flanking
Find flanking markers for a specified position
fill.geno
Fill holes in genotype data
effectscan
Plot estimated QTL effects across the whole genome
find.marker
Find marker closest to a specified position
addpair
Scan for an additional pair of QTL in a multiple-QTL model
geno.table
Create table of genotype distributions
find.pseudomarker
Find the pseudomarker closest to a specified position
convert.scantwo
Convert output from scantwo for R/qtl version 1.03 and earlier
findDupMarkers
Find markers with identical genotype data
est.map
Estimate genetic maps
getid
Pull out the individual identifiers from a cross
addqtl
Scan for an additional QTL in a multiple-QTL model
est.rf
Estimate pairwise recombination fractions
find.markerindex
Determine the numeric index for a marker
inferFounderHap
Crude reconstruction of founder haplotypes in multi-parent RIL
inferredpartitions
Identify inferred partitions in mapping QTL to a phylogenetic tree
argmax.geno
Reconstruct underlying genotypes
map2table
Convert genetic map from list to table.
makeqtl
Make a qtl object
mqmaugment
MQM augmentation
map10
An example genetic map
fitqtl
Fit a multiple-QTL model
mqmautocofactors
Automatic setting of cofactors, taking marker density into account
groupclusteredheatmap
Retrieving groups of traits after clustering
locations
Genetic locations of traits for the multitrait dataset
arithscan
Arithmetic operators for scanone and scantwo results
hyper
Data on hypertension
convert2riself
Convert a cross to RIL by selfing
mapthis
Simulated data for illustrating genetic map construction
dropfromqtl
Drop a QTL from a qtl object
mqmplot.clusteredheatmap
Plot clustered heatmap of MQM scan on multiple phenotypes
droponemarker
Drop one marker at a time and determine effect on genetic map
mqmextractmarkers
MQM marker extraction
mqmplot.cofactors
Plot cofactors on the genetic map
lodint
LOD support interval
mqmgetmodel
Retrieve the QTL model used in mapping from the results of an MQM scan
mqmfind.marker
Fetch significant markers after permutation analysis
movemarker
Move a marker to a new chromosome
max.scantwo
Maximum peak in two-dimensional genome scan
find.markerpos
Find position of a marker
mqmpermutation
Estimate QTL LOD score significance using permutations or simulations
mqmplot.directedqtl
Plot LOD*Effect curves of a multiple-QTL model
cbind.scantwoperm
Combine scantwo permutations by column
find.pheno
Find column number for a particular phenotype
checkAlleles
Identify markers with switched alleles
mqmplot.heatmap
Heatmap of a genome of MQM scan on multiple phenotypes
cim
Composite interval mapping
nmar
Determine the numbers of markers on each chromosome
mqmprocesspermutation
Convert mqmmulti objects into a scanoneperm object
mqmplot.singletrait
Plot LOD curves of a multiple-QTL model
mqmscanfdr
Estimate FDR for multiple trait QTL analysis
clean.cross
Remove derived data
phenames
Pull out the phenotypes names from a cross
mqmsetcofactors
Set cofactors at fixed intervals, to be used with MQM
convert2risib
Convert a cross to RIL by sib mating
geno.image
Plot grid of genotype data
geno.crosstab
Create table of two-locus genotypes
nmissing
Number of missing genotypes
interpPositions
Interpolate positions from one map to another
fake.4way
Simulated data for a 4-way cross
multitrait
Example Cross object from R/QTL with multiple traits
convert2sa
Convert a sex-specific map to a sex-averaged one
mqmtestnormal
Shapiro normality test used for MQM
nqtl
Determine the number of QTL in a QTL object
jittermap
Jitter marker positions in a genetic map
pickMarkerSubset
Identify the largest subset of markers that are some distance apart
markerlrt
General likelihood ratio test for association between marker pairs
ntyped
Number of genotypes
markernames
Pull out the marker names from a cross
fake.bc
Simulated data for a backcross
fitstahl
Fit Stahl interference model
mqmplot.multitrait
Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes
mqmplot.permutations
Plot results from mqmpermutation
flip.order
Flip the orders of markers on a set of chromosomes
mqmscan
Genome scan with a multiple QTL model (MQM)
formMarkerCovar
Create matrix of marker covariates for QTL analysis
listeria
Data on Listeria monocytogenes susceptibility
formLinkageGroups
Partition markers into linkage groups
mqmscanall
Parallelized MQM on multiple phenotypes in a cross object
max.scanPhyloQTL
Maximum peak in genome scan to map a QTL to a phylogenetic tree
nphe
Determine the number of phenotypes QTL experiment
plotMap
Plot genetic map
locateXO
Estimate locations of crossovers
nqrank
Transform a vector of quantitative values to the corresponding normal quantiles
plot.cross
Plot various features of a cross object
plotErrorlod
Plot grid of error LOD values
plotMissing
Plot grid of missing genotypes
plot.scanone
Plot LOD curves
plot.scanoneboot
Plot results of bootstrap for QTL position
plotGeno
Plot observed genotypes, flagging likely errors
plotPheno
Plot a phenotype distribution
plotInfo
Plot the proportion of missing genotype information
max.scanone
Maximum peak in genome scan
plotPXG
Plot phenotypes versus marker genotypes
pull.rf
Pull out recombination fractions or LOD scores from a cross object
plot.rfmatrix
Plot recombination fractions or LOD scores for a single marker
qtl-internal
Internal qtl functions
plot.scanPhyloQTL
Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree
mqmplot.circle
Circular genome plot for MQM
pull.map
Pull out the genetic map from a cross
pull.genoprob
Pull out the genotype probabilities from a cross
refineqtl
Refine the positions of QTL
mqmplot.cistrans
cis-trans plot
nchr
Determine the number of chromosomes
replacemap.scantwo
Replace the genetic map in QTL mapping results with an alternate map
replaceqtl
Replace a QTL in a qtl object with a different position
plotModel
Plot a QTL model
scanoneboot
Bootstrap to get interval estimate of QTL location
plot.scanoneperm
Plot permutation results for a single-QTL genome scan
reorderqtl
Reorder the QTL in a qtl object
scanqtl
General QTL scan
scanonevar
Genome scan for QTL affecting mean and/or variance
pull.argmaxgeno
Pull out the results of the Viterbi algorithm from a cross
nind
Determine the number of individuals QTL experiment
qtlversion
Installed version of R/qtl
scantwo
Two-dimensional genome scan with a two-QTL model
subset.cross
Subsetting data for QTL experiment
read.cross
Read data for a QTL experiment
plot.scantwo
Plot LOD scores for a two-dimensional genome scan
nullmarkers
Identify markers without any genotype data
subset.map
Subsetting chromosomes for a genetic map
orderMarkers
Find an initial order for markers within chromosomes
summary.ripple
Print summary of ripple results
rescalemap
Rescale genetic maps
strip.partials
Strip partially informative genotypes
stepwiseqtl
Stepwise selection for multiple QTL
ripple
Compare marker orders
summary.scanPhyloQTL
Summarize the results a genome scan to map a QTL to a phylogenetic tree
pull.markers
Drop all but a selected set of markers
summaryMap
Print summary of a genetic map
pull.pheno
Pull out phenotype data from a cross
replace.map
Replace the genetic map of a cross
plot.qtl
Plot QTL locations
scanPhyloQTL
Single-QTL genome scan to map QTL to a phylogenetic tree
switch.order
Switch the order of markers on a chromosome
replacemap.scanone
Replace the genetic map in QTL mapping results with an alternate map
plotRF
Plot recombination fractions
scantwopermhk
Permutation test for 2d genome scan by Haley-Knott regression
switchAlleles
Switch alleles at selected markers
summary.qtl
Print summary of a QTL object
simPhyloQTL
Simulate a set of intercrosses for a single diallelic QTL
scanone
Genome scan with a single QTL model
simulatemissingdata
Simulates missing genotype data
shiftmap
Shift starting points in genetic maps
subset.scanone
Subsetting the results of a genome scan
write.cross
Write data for a QTL experiment to a file
summaryScantwoOld
Summarize the results of a two-dimensional genome scan
xaxisloc.scanone
Get x-axis locations in scanone plot
summary.scantwoperm
LOD thresholds from scantwo permutation results
subset.scanoneperm
Subsetting permutation test results
plot.scantwoperm
Plot permutation results for a 2d, 2-QTL genome scan
plotLodProfile
Plot 1-d LOD profiles for a multiple QTL model
table2map
Convert a table of marker positions to a map object.
pull.draws
Pull out the genotype imputations from a cross
top.errorlod
List genotypes with large error LOD scores
pull.geno
Pull out the genotype data from a cross
sim.map
Simulate a genetic map
readMWril
Read data for 4- or 8-way RIL
totmar
Determine the total number of markers
reduce2grid
Reduce to a grid of pseudomarkers.
transformPheno
Transformation of the phenotypes in a cross object
scanonevar.meanperm
Permutation test for mean effect in scanonevar
scanonevar.varperm
Permutation test for variance effect in scanonevar
simFounderSnps
Simulate founder SNPs for a multiple-strain RIL
sim.cross
Simulate a QTL experiment
summary.cross
Print summary of QTL experiment
summary.scanoneperm
LOD thresholds from scanone permutation results
summary.fitqtl
Summary of fit of qtl model
summary.scantwo
Summarize the results of a two-dimensional genome scan
sim.geno
Simulate genotypes given observed marker data
tryallpositions
Test all possible positions for a marker
subset.scantwo
Subsetting the results of a 2-d genome scan
subset.scantwoperm
Subsetting two-dimensional permutation test results
summary.scanone
Summarize the results of a genome scans
typingGap
Maximum distance between genotyped markers
summary.scanoneboot
Bootstrap confidence interval for QTL location
addcovarint
Add QTL x covariate interaction to a multiple-QTL model
addint
Add pairwise interaction to a multiple-QTL model
add.threshold
Add significance threshold to plot
bristleX
Data on bristle number in Drosophila
bayesint
Bayesian credible interval