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qtl (version 1.21-2)
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
7,337
Version
1.21-2
License
GPL-3
Maintainer
Karl W Broman
Last Published
March 21st, 2011
Functions in qtl (1.21-2)
Search all functions
addqtl
Scan for an additional QTL in a multiple-QTL model
addcovarint
Add QTL x covariate interaction to a multiple-QTL model
bristleX
Data on bristle number in Drosophila
drop.markers
Drop a set of markers
countXO
Count number of obligate crossovers for each individual
find.markerindex
Determine the numeric index for a marker
A starting point
Introductory comments on R/qtl
checkAlleles
Identify markers with switched alleles
fitqtl
Fit a multiple-QTL model
mqmplot.cofactors
Plot cofactors on the genetic map
max.scanPhyloQTL
Maximum peak in genome scan to map a QTL to a phylogenetic tree
arithscan
Arithmetic operators for scanone and scantwo results
mqmfind.marker
Fetch significant markers after permutation analysis
badorder
An intercross with misplaced markers
clean.scantwo
Clean up scantwo output
arithscanperm
Arithmetic Operators for permutation results
geno.crosstab
Create table of two-locus genotypes
find.flanking
Find flanking markers for a specified position
nmar
Determine the numbers of markers on each chromosome
plot.scantwoperm
Plot permutation results for a 2d, 2-QTL genome scan
inferredpartitions
Identify inferred partitions in mapping QTL to a phylogenetic tree
compareorder
Compare two orderings of markers on a chromosome
fake.4way
Simulated data for a 4-way cross
orderMarkers
Find an initial order for markers within chromosomes
c.cross
Combine data for QTL experiments
replace.map
Replace the genetic map of a cross
mqmplot.cistrans
cis-trans plot
geno.table
Create table of genotype distributions
makeqtl
Make a qtl object
drop.nullmarkers
Drop markers without any genotype data
hyper
Data on hypertension
markernames
Pull out the marker names from a cross
chrlen
Chromosome lengths in QTL experiment
fitstahl
Fit Stahl interference model
c.scantwoperm
Combine data from scantwo permutations
c.scanone
Combine columns from multiple scanone results
comparegeno
Compare individuals' genotype data
nmissing
Number of missing genotypes
groupclusteredheatmap
Retrieving groups of traits after clustering
formLinkageGroups
Partition markers into linkage groups
effectscan
Plot estimated QTL effects across the whole genome
calc.penalties
Calculate LOD penalties
addtoqtl
Add to a qtl object
replaceqtl
Replace a QTL in a qtl object with a different position
mqmscan
Genome scan with a multiple QTL model (MQM)
c.scanoneperm
Combine data from scanone permutations
listeria
Data on Listeria monocytogenes susceptibility
addpair
Scan for an additional pair of QTL in a multiple-QTL model
calc.genoprob
Calculate conditional genotype probabilities
movemarker
Move a marker to a new chromosome
scanqtl
General QTL scan
plot.missing
Plot grid of missing genotypes
max.scanone
Maximum peak in genome scan
strip.partials
Strip partially informative genotypes
summary.scantwo
Summarize the results of a two-dimensional genome scan
mqmscanall
Parallelized MQM on multiple phenotypes in a cross object
pull.markers
Drop all but a selected set of markers
plot.scanoneboot
Plot results of bootstrap for QTL position
cim
Composite interval mapping
cbind.scanoneperm
Combine columns from multiple scanone permutation results
tryallpositions
Test all possible positions for a marker
plot.geno
Plot observed genotypes, flagging likely errors
pull.rf
Pull out recombination fractions or LOD scores from a cross object
shiftmap
Shift starting points in genetic maps
mqmextractmarkers
MQM marker extraction
mqmautocofactors
Automatic setting of cofactors, taking marker density into account
chrnames
Pull out the chromosome names from a cross
summary.scanone
Summarize the results of a genome scans
nchr
Determine the number of chromosomes
xaxisloc.scanone
Get x-axis locations in scanone plot
jittermap
Jitter marker positions in a genetic map
fake.bc
Simulated data for a backcross
mqmpermutation
Estimate QTL LOD score significance using permutations or simulations
qtlversion
Installed version of R/qtl
nqrank
Transform a vector of quantitative values to the corresponding normal quantiles
convert.map
Change map function for a genetic map
ntyped
Number of genotypes
subset.map
Subsetting chromosomes for a genetic map
summary.fitqtl
Summary of fit of qtl model
top.errorlod
List genotypes with large error LOD scores
plot.scanone
Plot LOD curves
plot.errorlod
Plot grid of error LOD values
mqmplot.clusteredheatmap
Plot clustered heatmap of MQM scan on multiple phenotypes
est.rf
Estimate pairwise recombination fractions
summary.scantwo.old
Summarize the results of a two-dimensional genome scan
mqmplot.heatmap
Heatmap of a genome of MQM scan on multiple phenotypes
subset.scantwo
Subsetting the results of a 2-d genome scan
plot.map
Plot genetic map
subset.scantwoperm
Subsetting two-dimensional permutation test results
rescalemap
Rescale genetic maps
nind
Determine the number of individuals QTL experiment
scanoneboot
Bootstrap to get interval estimate of QTL location
find.pseudomarker
Find the pseudomarker closest to a specified position
read.cross
Read data for a QTL experiment
scantwo
Two-dimensional genome scan with a two-QTL model
ripple
Compare marker orders
totmar
Determine the total number of markers
switchAlleles
Switch alleles at selected markers
mapthis
Simulated data for illustrating genetic map construction
mqmtestnormal
Shapiro normality test used for MQM
typingGap
Maximum distance between genotyped markers
summary.map
Print summary of a genetic map
summary.scanoneperm
LOD thresholds from scanone permutation results
drop.dupmarkers
Drop duplicate markers
switch.order
Switch the order of markers on a chromosome
mqmplot.multitrait
Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes
plot.scanPhyloQTL
Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree
plotModel
Plot a QTL model
mqmplot.permutations
Plot results from mqmpermutation
plot.scantwo
Plot LOD scores for a two-dimensional genome scan
pull.pheno
Pull out phenotype data from a cross
scanPhyloQTL
Single-QTL genome scan to map QTL to a phylogenetic tree
readMWril
Read data for 4- or 8-way RIL
sim.map
Simulate a genetic map
simulatemissingdata
Simulates missing genotype data
sim.cross
Simulate a QTL experiment
calc.errorlod
Identify likely genotyping errors
dropfromqtl
Drop a QTL from a qtl object
condense.scantwo
Condense the output from a 2-d genome scan
mqmaugment
MQM augmentation
plot.rf
Plot recombination fractions
mqmscanfdr
Estimate FDR for multiple trait QTL analysis
reorderqtl
Reorder the QTL in a qtl object
summary.cross
Print summary of QTL experiment
subset.scanoneperm
Subsetting permutation test results
add.cim.covar
Indicate marker covariates from composite interval mapping
allchrsplits
Test all possible splits of a chromosome into two pieces
bayesint
Bayesian credible interval
c.scantwo
Combine columns from multiple scantwo results
cleanGeno
Delete genotypes that are possibly in error
convert2sa
Convert a sex-specific map to a sex-averaged one
locateXO
Estimate locations of crossovers
plot.pxg
Plot phenotypes versus marker genotypes
phenames
Pull out the phenotypes names from a cross
pull.map
Pull out the genetic map from a cross
scanone
Genome scan with a single QTL model
sim.geno
Simulate genotypes given observed marker data
subset.scanone
Subsetting the results of a genome scan
summary.scantwoperm
LOD thresholds from scantwo permutation results
add.threshold
Add significance threshold to plot
addint
Add pairwise interaction to a multiple-QTL model
convert.scantwo
Convert output from scantwo for R/qtl version 1.03 and earlier
convert2risib
Convert a cross to RIL by sib mating
find.markerpos
Find position of a marker
findDupMarkers
Find markers with identical genotype data
getid
Pull out the individual identifiers from a cross
map10
An example genetic map
mqmprocesspermutation
Convert mqmmulti objects into a scanoneperm object
locations
Genetic locations of traits for the multitrait dataset
nphe
Determine the number of phenotypes QTL experiment
refineqtl
Refine the positions of QTL
replacemap.scanone
Replace the genetic map in QTL mapping results with an alternate map
convert2riself
Convert a cross to RIL by selfing
clean.cross
Remove derived data
find.pheno
Find column number for a particular phenotype
markerlrt
General likelihood ratio test for association between marker pairs
lodint
LOD support interval
mqmplot.circle
Circular genome plot for MQM
plot.qtl
Plot QTL locations
plot.pheno
Plot a phenotype distribution
simFounderSnps
Simulate founder SNPs for a multiple-strain RIL
transformPheno
Transformation of the phenotypes in a cross object
comparecrosses
Compare two cross objects
mqmsetcofactors
Set cofactors at fixed intervals, to be used with MQM
plotLodProfile
Plot 1-d LOD profiles for a multiple QTL model
replacemap.scantwo
Replace the genetic map in QTL mapping results with an alternate map
stepwiseqtl
Stepwise selection for multiple QTL
summary.ripple
Print summary of ripple results
summary.scanoneboot
Bootstrap confidence interval for QTL location
write.cross
Write data for a QTL experiment to a file
MQM
Introduction to Multiple QTL Model (MQM) mapping
argmax.geno
Reconstruct underlying genotypes
convert.scanone
Convert output from scanone for R/qtl version 0.98
bristle3
Data on bristle number in Drosophila
geno.image
Plot grid of genotype data
mqmplot.directedqtl
Plot LOD*Effect curves of a multiple-QTL model
effectplot
Plot phenotype means against genotypes at one or two markers
est.map
Estimate genetic maps
mqmplot.singletrait
Plot LOD curves of a multiple-QTL model
plot.info
Plot the proportion of missing genotype information
plot.cross
Plot various features of a cross object
plot.rfmatrix
Plot recombination fractions or LOD scores for a single marker
qtl-internal
Internal qtl functions
summary.qtl
Print summary of a QTL object
simPhyloQTL
Simulate a set of intercrosses for a single diallelic QTL
max.scantwo
Maximum peak in two-dimensional genome scan
find.marker
Find marker closest to a specified position
fill.geno
Fill holes in genotype data
addloctocross
Add phenotype location into a cross object
summary.scanPhyloQTL
Summarize the results a genome scan to map a QTL to a phylogenetic tree
pull.geno
Pull out the genotype data from a cross
fake.f2
Simulated data for an F2 intercross
subset.cross
Subsetting data for QTL experiment
droponemarker
Drop one marker at a time and determine effect on genetic map
multitrait
Example Cross object from R/QTL with multiple traits
plot.scanoneperm
Plot permutation results for a single-QTL genome scan
mqmgetmodel
Retrieve the QTL model used in mapping from the results of an MQM scan