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qtl (version 1.39-5)
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
5,002
Version
1.39-5
License
GPL-3
Maintainer
Karl W Broman
Last Published
March 4th, 2016
Functions in qtl (1.39-5)
Search all functions
checkAlleles
Identify markers with switched alleles
max.scantwo
Maximum peak in two-dimensional genome scan
nmar
Determine the numbers of markers on each chromosome
scanonevar
Genome scan for QTL affecting mean and/or variance
A starting point
Introductory comments on R/qtl
convert2riself
Convert a cross to RIL by selfing
chrnames
Pull out the chromosome names from a cross
scanone
Genome scan with a single QTL model
markerlrt
General likelihood ratio test for association between marker pairs
add.threshold
Add significance threshold to plot
plot.scanoneboot
Plot results of bootstrap for QTL position
compareorder
Compare two orderings of markers on a chromosome
est.map
Estimate genetic maps
top.errorlod
List genotypes with large error LOD scores
multitrait
Example Cross object from R/QTL with multiple traits
write.cross
Write data for a QTL experiment to a file
dropfromqtl
Drop a QTL from a qtl object
fake.f2
Simulated data for an F2 intercross
mqmplot.singletrait
Plot LOD curves of a multiple-QTL model
transformPheno
Transformation of the phenotypes in a cross object
mqmscanfdr
Estimate FDR for multiple trait QTL analysis
convert2risib
Convert a cross to RIL by sib mating
argmax.geno
Reconstruct underlying genotypes
plot.scanone
Plot LOD curves
fitqtl
Fit a multiple-QTL model
plotErrorlod
Plot grid of error LOD values
lodint
LOD support interval
plotRF
Plot recombination fractions
comparecrosses
Compare two cross objects
formLinkageGroups
Partition markers into linkage groups
totmar
Determine the total number of markers
getid
Pull out the individual identifiers from a cross
replacemap.scanone
Replace the genetic map in QTL mapping results with an alternate map
cim
Composite interval mapping
map2table
Convert genetic map from list to table.
addcovarint
Add QTL x covariate interaction to a multiple-QTL model
mapthis
Simulated data for illustrating genetic map construction
badorder
An intercross with misplaced markers
pull.pheno
Pull out phenotype data from a cross
formMarkerCovar
Create matrix of marker covariates for QTL analysis
c.scanoneperm
Combine data from scanone permutations
find.markerindex
Determine the numeric index for a marker
clean.scantwo
Clean up scantwo output
calc.errorlod
Identify likely genotyping errors
c.scantwo
Combine columns from multiple scantwo results
addmarker
Add a marker to a cross
ripple
Compare marker orders
qtlversion
Installed version of R/qtl
clean.cross
Remove derived data
drop.nullmarkers
Drop markers without any genotype data
hyper
Data on hypertension
scanqtl
General QTL scan
summary.scanoneboot
Bootstrap confidence interval for QTL location
fake.bc
Simulated data for a backcross
condense.scantwo
Condense the output from a 2-d genome scan
convert2sa
Convert a sex-specific map to a sex-averaged one
max.scanone
Maximum peak in genome scan
mqmfind.marker
Fetch significant markers after permutation analysis
geno.image
Plot grid of genotype data
find.pheno
Find column number for a particular phenotype
summaryScantwoOld
Summarize the results of a two-dimensional genome scan
mqmplot.clusteredheatmap
Plot clustered heatmap of MQM scan on multiple phenotypes
convert.scanone
Convert output from scanone for R/qtl version 0.98
plotInfo
Plot the proportion of missing genotype information
findDupMarkers
Find markers with identical genotype data
drop.markers
Drop a set of markers
MQM
Introduction to Multiple QTL Model (MQM) mapping
table2map
Convert a table of marker positions to a map object.
max.scanPhyloQTL
Maximum peak in genome scan to map a QTL to a phylogenetic tree
qtl-internal
Internal qtl functions
effectplot
Plot phenotype means against genotypes at one or two markers
read.cross
Read data for a QTL experiment
arithscan
Arithmetic operators for scanone and scantwo results
mqmaugment
MQM augmentation
nqrank
Transform a vector of quantitative values to the corresponding normal quantiles
phenames
Pull out the phenotypes names from a cross
cbind.scanoneperm
Combine columns from multiple scanone permutation results
ntyped
Number of genotypes
cbind.scantwoperm
Combine scantwo permutations by column
calc.penalties
Calculate LOD penalties
mqmplot.heatmap
Heatmap of a genome of MQM scan on multiple phenotypes
plotMissing
Plot grid of missing genotypes
mqmautocofactors
Automatic setting of cofactors, taking marker density into account
fitstahl
Fit Stahl interference model
inferFounderHap
Crude reconstruction of founder haplotypes in multi-parent RIL
mqmplot.multitrait
Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes
simPhyloQTL
Simulate a set of intercrosses for a single diallelic QTL
nchr
Determine the number of chromosomes
arithscanperm
Arithmetic Operators for permutation results
mqmplot.permutations
Plot results from mqmpermutation
plot.cross
Plot various features of a cross object
locateXO
Estimate locations of crossovers
bayesint
Bayesian credible interval
plotModel
Plot a QTL model
nphe
Determine the number of phenotypes QTL experiment
summary.scantwo
Summarize the results of a two-dimensional genome scan
pull.genoprob
Pull out the genotype probabilities from a cross
pull.draws
Pull out the genotype imputations from a cross
fake.4way
Simulated data for a 4-way cross
subset.map
Subsetting chromosomes for a genetic map
makeqtl
Make a qtl object
cleanGeno
Delete genotypes that are possibly in error
mqmextractmarkers
MQM marker extraction
geno.table
Create table of genotype distributions
pull.geno
Pull out the genotype data from a cross
convert.scantwo
Convert output from scantwo for R/qtl version 1.03 and earlier
addint
Add pairwise interaction to a multiple-QTL model
mqmsetcofactors
Set cofactors at fixed intervals, to be used with MQM
mqmscan
Genome scan with a multiple QTL model (MQM)
bristle3
Data on bristle number in Drosophila
jittermap
Jitter marker positions in a genetic map
addtoqtl
Add to a qtl object
replaceqtl
Replace a QTL in a qtl object with a different position
chrlen
Chromosome lengths in QTL experiment
inferredpartitions
Identify inferred partitions in mapping QTL to a phylogenetic tree
find.marker
Find marker closest to a specified position
nullmarkers
Identify markers without any genotype data
drop.dupmarkers
Drop duplicate markers
fill.geno
Fill holes in genotype data
scanPhyloQTL
Single-QTL genome scan to map QTL to a phylogenetic tree
markernames
Pull out the marker names from a cross
plotPheno
Plot a phenotype distribution
map10
An example genetic map
scanonevar.varperm
Permutation test for variance effect in scanonevar
scanonevar.meanperm
Permutation test for mean effect in scanonevar
simulatemissingdata
Simulates missing genotype data
summary.scanone
Summarize the results of a genome scans
mqmprocesspermutation
Convert mqmmulti objects into a scanoneperm object
c.cross
Combine data for QTL experiments
find.pseudomarker
Find the pseudomarker closest to a specified position
est.rf
Estimate pairwise recombination fractions
readMWril
Read data for 4- or 8-way RIL
addqtl
Scan for an additional QTL in a multiple-QTL model
mqmplot.circle
Circular genome plot for MQM
plot.qtl
Plot QTL locations
add.cim.covar
Indicate marker covariates from composite interval mapping
geno.crosstab
Create table of two-locus genotypes
replacemap.scantwo
Replace the genetic map in QTL mapping results with an alternate map
subset.scantwo
Subsetting the results of a 2-d genome scan
nind
Determine the number of individuals QTL experiment
listeria
Data on Listeria monocytogenes susceptibility
flip.order
Flip the orders of markers on a set of chromosomes
calc.genoprob
Calculate conditional genotype probabilities
subset.cross
Subsetting data for QTL experiment
switch.order
Switch the order of markers on a chromosome
addpair
Scan for an additional pair of QTL in a multiple-QTL model
groupclusteredheatmap
Retrieving groups of traits after clustering
locations
Genetic locations of traits for the multitrait dataset
mqmscanall
Parallelized MQM on multiple phenotypes in a cross object
sim.geno
Simulate genotypes given observed marker data
addloctocross
Add phenotype location into a cross object
effectscan
Plot estimated QTL effects across the whole genome
refineqtl
Refine the positions of QTL
mqmtestnormal
Shapiro normality test used for MQM
interpPositions
Interpolate positions from one map to another
pull.markers
Drop all but a selected set of markers
find.markerpos
Find position of a marker
mqmpermutation
Estimate QTL LOD score significance using permutations or simulations
reduce2grid
Reduce to a grid of pseudomarkers.
pull.map
Pull out the genetic map from a cross
pull.rf
Pull out recombination fractions or LOD scores from a cross object
scantwo
Two-dimensional genome scan with a two-QTL model
pickMarkerSubset
Identify the largest subset of markers that are some distance apart
reorderqtl
Reorder the QTL in a qtl object
orderMarkers
Find an initial order for markers within chromosomes
summary.cross
Print summary of QTL experiment
summary.qtl
Print summary of a QTL object
comparegeno
Compare individuals' genotype data
bristleX
Data on bristle number in Drosophila
subset.scanoneperm
Subsetting permutation test results
allchrsplits
Test all possible splits of a chromosome into two pieces
tryallpositions
Test all possible positions for a marker
replace.map
Replace the genetic map of a cross
subset.scantwoperm
Subsetting two-dimensional permutation test results
simFounderSnps
Simulate founder SNPs for a multiple-strain RIL
strip.partials
Strip partially informative genotypes
convert.map
Change map function for a genetic map
droponemarker
Drop one marker at a time and determine effect on genetic map
sim.cross
Simulate a QTL experiment
plot.scantwo
Plot LOD scores for a two-dimensional genome scan
summary.fitqtl
Summary of fit of qtl model
c.scanone
Combine columns from multiple scanone results
mqmplot.cistrans
cis-trans plot
c.scantwoperm
Combine data from scantwo permutations
countXO
Count number of obligate crossovers for each individual
stepwiseqtl
Stepwise selection for multiple QTL
rescalemap
Rescale genetic maps
find.flanking
Find flanking markers for a specified position
movemarker
Move a marker to a new chromosome
switchAlleles
Switch alleles at selected markers
nqtl
Determine the number of QTL in a QTL object
mqmplot.directedqtl
Plot LOD*Effect curves of a multiple-QTL model
subset.scanone
Subsetting the results of a genome scan
nmissing
Number of missing genotypes
plotPXG
Plot phenotypes versus marker genotypes
plot.scanPhyloQTL
Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree
shiftmap
Shift starting points in genetic maps
plot.rfmatrix
Plot recombination fractions or LOD scores for a single marker
summary.scantwoperm
LOD thresholds from scantwo permutation results
summaryMap
Print summary of a genetic map
scantwopermhk
Permutation test for 2d genome scan by Haley-Knott regression
sim.map
Simulate a genetic map
plotMap
Plot genetic map
mqmgetmodel
Retrieve the QTL model used in mapping from the results of an MQM scan
mqmplot.cofactors
Plot cofactors on the genetic map
plotGeno
Plot observed genotypes, flagging likely errors
plotLodProfile
Plot 1-d LOD profiles for a multiple QTL model
plot.scanoneperm
Plot permutation results for a single-QTL genome scan
pull.argmaxgeno
Pull out the results of the Viterbi algorithm from a cross
plot.scantwoperm
Plot permutation results for a 2d, 2-QTL genome scan
scanoneboot
Bootstrap to get interval estimate of QTL location
summary.ripple
Print summary of ripple results
summary.scanoneperm
LOD thresholds from scanone permutation results
summary.scanPhyloQTL
Summarize the results a genome scan to map a QTL to a phylogenetic tree
xaxisloc.scanone
Get x-axis locations in scanone plot
typingGap
Maximum distance between genotyped markers