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qtl (version 1.31-9)
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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Install
install.packages('qtl')
Monthly Downloads
5,612
Version
1.31-9
License
GPL-3
Maintainer
Karl W Broman
Last Published
March 20th, 2014
Functions in qtl (1.31-9)
Search all functions
readMWril
Read data for 4- or 8-way RIL
cleanGeno
Delete genotypes that are possibly in error
convert.map
Change map function for a genetic map
locations
Genetic locations of traits for the multitrait dataset
shiftmap
Shift starting points in genetic maps
comparegeno
Compare individuals' genotype data
qtl-internal
Internal qtl functions
plotPXG
Plot phenotypes versus marker genotypes
A starting point
Introductory comments on R/qtl
addint
Add pairwise interaction to a multiple-QTL model
calc.errorlod
Identify likely genotyping errors
bristleX
Data on bristle number in Drosophila
bayesint
Bayesian credible interval
compareorder
Compare two orderings of markers on a chromosome
find.markerindex
Determine the numeric index for a marker
addcovarint
Add QTL x covariate interaction to a multiple-QTL model
MQM
Introduction to Multiple QTL Model (MQM) mapping
countXO
Count number of obligate crossovers for each individual
convert.scanone
Convert output from scanone for R/qtl version 0.98
lodint
LOD support interval
effectplot
Plot phenotype means against genotypes at one or two markers
arithscanperm
Arithmetic Operators for permutation results
effectscan
Plot estimated QTL effects across the whole genome
addqtl
Scan for an additional QTL in a multiple-QTL model
calc.penalties
Calculate LOD penalties
convert2risib
Convert a cross to RIL by sib mating
addtoqtl
Add to a qtl object
geno.table
Create table of genotype distributions
c.scantwo
Combine columns from multiple scantwo results
mqmplot.clusteredheatmap
Plot clustered heatmap of MQM scan on multiple phenotypes
convert2riself
Convert a cross to RIL by selfing
drop.dupmarkers
Drop duplicate markers
fake.4way
Simulated data for a 4-way cross
find.pseudomarker
Find the pseudomarker closest to a specified position
scanone
Genome scan with a single QTL model
arithscan
Arithmetic operators for scanone and scantwo results
badorder
An intercross with misplaced markers
droponemarker
Drop one marker at a time and determine effect on genetic map
mqmplot.singletrait
Plot LOD curves of a multiple-QTL model
fake.f2
Simulated data for an F2 intercross
cbind.scanoneperm
Combine columns from multiple scanone permutation results
mqmfind.marker
Fetch significant markers after permutation analysis
fake.bc
Simulated data for a backcross
convert.scantwo
Convert output from scantwo for R/qtl version 1.03 and earlier
mqmgetmodel
Retrieve the QTL model used in mapping from the results of an MQM scan
est.rf
Estimate pairwise recombination fractions
checkAlleles
Identify markers with switched alleles
argmax.geno
Reconstruct underlying genotypes
c.scantwoperm
Combine data from scantwo permutations
formLinkageGroups
Partition markers into linkage groups
formMarkerCovar
Create matrix of marker covariates for QTL analysis
dropfromqtl
Drop a QTL from a qtl object
bristle3
Data on bristle number in Drosophila
clean.scantwo
Clean up scantwo output
addmarker
Add a marker to a cross
nmar
Determine the numbers of markers on each chromosome
locateXO
Estimate locations of crossovers
c.scanoneperm
Combine data from scanone permutations
geno.crosstab
Create table of two-locus genotypes
mqmaugment
MQM augmentation
addpair
Scan for an additional pair of QTL in a multiple-QTL model
drop.markers
Drop a set of markers
stepwiseqtl
Stepwise selection for multiple QTL
condense.scantwo
Condense the output from a 2-d genome scan
c.scanone
Combine columns from multiple scanone results
mqmplot.cofactors
Plot cofactors on the genetic map
geno.image
Plot grid of genotype data
cim
Composite interval mapping
simulatemissingdata
Simulates missing genotype data
est.map
Estimate genetic maps
drop.nullmarkers
Drop markers without any genotype data
find.pheno
Find column number for a particular phenotype
nchr
Determine the number of chromosomes
max.scanPhyloQTL
Maximum peak in genome scan to map a QTL to a phylogenetic tree
c.cross
Combine data for QTL experiments
interpPositions
Interpolate positions from one map to another
pull.geno
Pull out the genotype data from a cross
plot.rfmatrix
Plot recombination fractions or LOD scores for a single marker
sim.map
Simulate a genetic map
mqmplot.heatmap
Heatmap of a genome of MQM scan on multiple phenotypes
map10
An example genetic map
clean.cross
Remove derived data
read.cross
Read data for a QTL experiment
fill.geno
Fill holes in genotype data
mqmplot.directedqtl
Plot LOD*Effect curves of a multiple-QTL model
orderMarkers
Find an initial order for markers within chromosomes
max.scantwo
Maximum peak in two-dimensional genome scan
comparecrosses
Compare two cross objects
subset.map
Subsetting chromosomes for a genetic map
convert2sa
Convert a sex-specific map to a sex-averaged one
mqmautocofactors
Automatic setting of cofactors, taking marker density into account
mqmextractmarkers
MQM marker extraction
listeria
Data on Listeria monocytogenes susceptibility
mqmscanall
Parallelized MQM on multiple phenotypes in a cross object
reorderqtl
Reorder the QTL in a qtl object
plot.qtl
Plot QTL locations
jittermap
Jitter marker positions in a genetic map
mqmplot.permutations
Plot results from mqmpermutation
simFounderSnps
Simulate founder SNPs for a multiple-strain RIL
scanPhyloQTL
Single-QTL genome scan to map QTL to a phylogenetic tree
subset.scanone
Subsetting the results of a genome scan
scanoneboot
Bootstrap to get interval estimate of QTL location
getid
Pull out the individual identifiers from a cross
plotModel
Plot a QTL model
summary.fitqtl
Summary of fit of qtl model
mqmtestnormal
Shapiro normality test used for MQM
pull.pheno
Pull out phenotype data from a cross
mqmsetcofactors
Set cofactors at fixed intervals, to be used with MQM
mqmscan
Genome scan with a multiple QTL model (MQM)
summary.scanoneboot
Bootstrap confidence interval for QTL location
fitstahl
Fit Stahl interference model
summary.scanone
Summarize the results of a genome scans
mapthis
Simulated data for illustrating genetic map construction
nqrank
Transform a vector of quantitative values to the corresponding normal quantiles
pull.argmaxgeno
Pull out the results of the Viterbi algorithm from a cross
multitrait
Example Cross object from R/QTL with multiple traits
movemarker
Move a marker to a new chromosome
groupclusteredheatmap
Retrieving groups of traits after clustering
nqtl
Determine the number of QTL in a QTL object
plotMap
Plot genetic map
summary.scanPhyloQTL
Summarize the results a genome scan to map a QTL to a phylogenetic tree
pull.genoprob
Pull out the genotype probabilities from a cross
max.scanone
Maximum peak in genome scan
replacemap.scanone
Replace the genetic map in QTL mapping results with an alternate map
qtlversion
Installed version of R/qtl
nind
Determine the number of individuals QTL experiment
markerlrt
General likelihood ratio test for association between marker pairs
plotMissing
Plot grid of missing genotypes
summaryScantwoOld
Summarize the results of a two-dimensional genome scan
transformPheno
Transformation of the phenotypes in a cross object
reduce2grid
Reduce to a grid of pseudomarkers.
inferredpartitions
Identify inferred partitions in mapping QTL to a phylogenetic tree
plot.scanone
Plot LOD curves
pull.markers
Drop all but a selected set of markers
mqmscanfdr
Estimate FDR for multiple trait QTL analysis
plot.scanoneboot
Plot results of bootstrap for QTL position
nmissing
Number of missing genotypes
replacemap.scantwo
Replace the genetic map in QTL mapping results with an alternate map
scantwo
Two-dimensional genome scan with a two-QTL model
plot.cross
Plot various features of a cross object
scanqtl
General QTL scan
switchAlleles
Switch alleles at selected markers
write.cross
Write data for a QTL experiment to a file
simPhyloQTL
Simulate a set of intercrosses for a single diallelic QTL
ripple
Compare marker orders
plot.scanPhyloQTL
Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree
refineqtl
Refine the positions of QTL
phenames
Pull out the phenotypes names from a cross
mqmplot.circle
Circular genome plot for MQM
pull.draws
Pull out the genotype imputations from a cross
nphe
Determine the number of phenotypes QTL experiment
makeqtl
Make a qtl object
ntyped
Number of genotypes
plotGeno
Plot observed genotypes, flagging likely errors
typingGap
Maximum distance between genotyped markers
pickMarkerSubset
Identify the largest subset of markers that are some distance apart
summary.cross
Print summary of QTL experiment
plotErrorlod
Plot grid of error LOD values
plot.scantwoperm
Plot permutation results for a 2d, 2-QTL genome scan
mqmplot.cistrans
cis-trans plot
pull.map
Pull out the genetic map from a cross
replaceqtl
Replace a QTL in a qtl object with a different position
plot.scantwo
Plot LOD scores for a two-dimensional genome scan
plotRF
Plot recombination fractions
pull.rf
Pull out recombination fractions or LOD scores from a cross object
plotLodProfile
Plot 1-d LOD profiles for a multiple QTL model
sim.cross
Simulate a QTL experiment
totmar
Determine the total number of markers
summary.scanoneperm
LOD thresholds from scanone permutation results
strip.partials
Strip partially informative genotypes
nullmarkers
Identify markers without any genotype data
plotPheno
Plot a phenotype distribution
summary.scantwo
Summarize the results of a two-dimensional genome scan
summary.ripple
Print summary of ripple results
rescalemap
Rescale genetic maps
subset.scanoneperm
Subsetting permutation test results
switch.order
Switch the order of markers on a chromosome
top.errorlod
List genotypes with large error LOD scores
tryallpositions
Test all possible positions for a marker
find.marker
Find marker closest to a specified position
plotInfo
Plot the proportion of missing genotype information
mqmplot.multitrait
Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes
find.flanking
Find flanking markers for a specified position
fitqtl
Fit a multiple-QTL model
chrlen
Chromosome lengths in QTL experiment
findDupMarkers
Find markers with identical genotype data
plot.scanoneperm
Plot permutation results for a single-QTL genome scan
sim.geno
Simulate genotypes given observed marker data
subset.scantwoperm
Subsetting two-dimensional permutation test results
summary.scantwoperm
LOD thresholds from scantwo permutation results
summaryMap
Print summary of a genetic map
summary.qtl
Print summary of a QTL object
mqmpermutation
Estimate QTL LOD score significance using permutations or simulations
add.threshold
Add significance threshold to plot
addloctocross
Add phenotype location into a cross object
find.markerpos
Find position of a marker
calc.genoprob
Calculate conditional genotype probabilities
markernames
Pull out the marker names from a cross
replace.map
Replace the genetic map of a cross
subset.scantwo
Subsetting the results of a 2-d genome scan
xaxisloc.scanone
Get x-axis locations in scanone plot
add.cim.covar
Indicate marker covariates from composite interval mapping
allchrsplits
Test all possible splits of a chromosome into two pieces
chrnames
Pull out the chromosome names from a cross
inferFounderHap
Crude reconstruction of founder haplotypes in multi-parent RIL
hyper
Data on hypertension
mqmprocesspermutation
Convert mqmmulti objects into a scanoneperm object
subset.cross
Subsetting data for QTL experiment