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qtl (version 1.38-4)
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
3,520
Version
1.38-4
License
GPL-3
Maintainer
Karl W Broman
Last Published
December 3rd, 2015
Functions in qtl (1.38-4)
Search all functions
MQM
Introduction to Multiple QTL Model (MQM) mapping
checkAlleles
Identify markers with switched alleles
allchrsplits
Test all possible splits of a chromosome into two pieces
convert2sa
Convert a sex-specific map to a sex-averaged one
drop.nullmarkers
Drop markers without any genotype data
c.scantwo
Combine columns from multiple scantwo results
plotErrorlod
Plot grid of error LOD values
convert.map
Change map function for a genetic map
cbind.scanoneperm
Combine columns from multiple scanone permutation results
read.cross
Read data for a QTL experiment
locateXO
Estimate locations of crossovers
dropfromqtl
Drop a QTL from a qtl object
replacemap.scantwo
Replace the genetic map in QTL mapping results with an alternate map
effectplot
Plot phenotype means against genotypes at one or two markers
condense.scantwo
Condense the output from a 2-d genome scan
qtl-internal
Internal qtl functions
fake.4way
Simulated data for a 4-way cross
scanqtl
General QTL scan
convert2risib
Convert a cross to RIL by sib mating
nmar
Determine the numbers of markers on each chromosome
geno.crosstab
Create table of two-locus genotypes
addpair
Scan for an additional pair of QTL in a multiple-QTL model
plotPheno
Plot a phenotype distribution
summary.scanPhyloQTL
Summarize the results a genome scan to map a QTL to a phylogenetic tree
mqmfind.marker
Fetch significant markers after permutation analysis
mqmscanfdr
Estimate FDR for multiple trait QTL analysis
drop.markers
Drop a set of markers
find.markerindex
Determine the numeric index for a marker
mqmextractmarkers
MQM marker extraction
nqrank
Transform a vector of quantitative values to the corresponding normal quantiles
countXO
Count number of obligate crossovers for each individual
markernames
Pull out the marker names from a cross
chrlen
Chromosome lengths in QTL experiment
add.threshold
Add significance threshold to plot
pull.markers
Drop all but a selected set of markers
argmax.geno
Reconstruct underlying genotypes
mqmplot.cofactors
Plot cofactors on the genetic map
mqmplot.permutations
Plot results from mqmpermutation
summaryScantwoOld
Summarize the results of a two-dimensional genome scan
summary.scantwoperm
LOD thresholds from scantwo permutation results
pull.genoprob
Pull out the genotype probabilities from a cross
nqtl
Determine the number of QTL in a QTL object
scanPhyloQTL
Single-QTL genome scan to map QTL to a phylogenetic tree
c.scantwoperm
Combine data from scantwo permutations
summary.qtl
Print summary of a QTL object
plot.scanPhyloQTL
Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree
cleanGeno
Delete genotypes that are possibly in error
comparegeno
Compare individuals' genotype data
cbind.scantwoperm
Combine scantwo permutations by column
plotInfo
Plot the proportion of missing genotype information
plotModel
Plot a QTL model
clean.cross
Remove derived data
pull.draws
Pull out the genotype imputations from a cross
subset.scanone
Subsetting the results of a genome scan
sim.map
Simulate a genetic map
formMarkerCovar
Create matrix of marker covariates for QTL analysis
map2table
Convert genetic map from list to table.
subset.cross
Subsetting data for QTL experiment
comparecrosses
Compare two cross objects
pull.map
Pull out the genetic map from a cross
addtoqtl
Add to a qtl object
convert.scanone
Convert output from scanone for R/qtl version 0.98
arithscan
Arithmetic operators for scanone and scantwo results
addloctocross
Add phenotype location into a cross object
mqmsetcofactors
Set cofactors at fixed intervals, to be used with MQM
bayesint
Bayesian credible interval
mqmtestnormal
Shapiro normality test used for MQM
reorderqtl
Reorder the QTL in a qtl object
find.pseudomarker
Find the pseudomarker closest to a specified position
nind
Determine the number of individuals QTL experiment
calc.errorlod
Identify likely genotyping errors
rescalemap
Rescale genetic maps
arithscanperm
Arithmetic Operators for permutation results
geno.table
Create table of genotype distributions
movemarker
Move a marker to a new chromosome
bristle3
Data on bristle number in Drosophila
mapthis
Simulated data for illustrating genetic map construction
write.cross
Write data for a QTL experiment to a file
mqmplot.circle
Circular genome plot for MQM
plot.scanone
Plot LOD curves
ntyped
Number of genotypes
addint
Add pairwise interaction to a multiple-QTL model
strip.partials
Strip partially informative genotypes
orderMarkers
Find an initial order for markers within chromosomes
addcovarint
Add QTL x covariate interaction to a multiple-QTL model
nmissing
Number of missing genotypes
calc.genoprob
Calculate conditional genotype probabilities
A starting point
Introductory comments on R/qtl
calc.penalties
Calculate LOD penalties
mqmaugment
MQM augmentation
nullmarkers
Identify markers without any genotype data
fake.f2
Simulated data for an F2 intercross
summary.scanone
Summarize the results of a genome scans
bristleX
Data on bristle number in Drosophila
plotPXG
Plot phenotypes versus marker genotypes
plotMap
Plot genetic map
findDupMarkers
Find markers with identical genotype data
hyper
Data on hypertension
addqtl
Scan for an additional QTL in a multiple-QTL model
addmarker
Add a marker to a cross
jittermap
Jitter marker positions in a genetic map
plot.rfmatrix
Plot recombination fractions or LOD scores for a single marker
summary.scanoneboot
Bootstrap confidence interval for QTL location
transformPheno
Transformation of the phenotypes in a cross object
convert.scantwo
Convert output from scantwo for R/qtl version 1.03 and earlier
find.marker
Find marker closest to a specified position
est.map
Estimate genetic maps
droponemarker
Drop one marker at a time and determine effect on genetic map
clean.scantwo
Clean up scantwo output
max.scanone
Maximum peak in genome scan
fill.geno
Fill holes in genotype data
geno.image
Plot grid of genotype data
est.rf
Estimate pairwise recombination fractions
mqmplot.cistrans
cis-trans plot
add.cim.covar
Indicate marker covariates from composite interval mapping
find.pheno
Find column number for a particular phenotype
convert2riself
Convert a cross to RIL by selfing
replace.map
Replace the genetic map of a cross
plot.cross
Plot various features of a cross object
fake.bc
Simulated data for a backcross
summary.ripple
Print summary of ripple results
flip.order
Flip the orders of markers on a set of chromosomes
locations
Genetic locations of traits for the multitrait dataset
formLinkageGroups
Partition markers into linkage groups
plot.scanoneboot
Plot results of bootstrap for QTL position
lodint
LOD support interval
interpPositions
Interpolate positions from one map to another
chrnames
Pull out the chromosome names from a cross
summary.scantwo
Summarize the results of a two-dimensional genome scan
max.scanPhyloQTL
Maximum peak in genome scan to map a QTL to a phylogenetic tree
c.scanone
Combine columns from multiple scanone results
effectscan
Plot estimated QTL effects across the whole genome
plot.scantwo
Plot LOD scores for a two-dimensional genome scan
c.scanoneperm
Combine data from scanone permutations
mqmautocofactors
Automatic setting of cofactors, taking marker density into account
pull.rf
Pull out recombination fractions or LOD scores from a cross object
find.flanking
Find flanking markers for a specified position
shiftmap
Shift starting points in genetic maps
makeqtl
Make a qtl object
listeria
Data on Listeria monocytogenes susceptibility
mqmplot.singletrait
Plot LOD curves of a multiple-QTL model
drop.dupmarkers
Drop duplicate markers
subset.scantwo
Subsetting the results of a 2-d genome scan
plot.scantwoperm
Plot permutation results for a 2d, 2-QTL genome scan
c.cross
Combine data for QTL experiments
mqmplot.heatmap
Heatmap of a genome of MQM scan on multiple phenotypes
sim.cross
Simulate a QTL experiment
markerlrt
General likelihood ratio test for association between marker pairs
reduce2grid
Reduce to a grid of pseudomarkers.
replacemap.scanone
Replace the genetic map in QTL mapping results with an alternate map
cim
Composite interval mapping
scanonevar
Genome scan for QTL affecting mean and/or variance
getid
Pull out the individual identifiers from a cross
mqmprocesspermutation
Convert mqmmulti objects into a scanoneperm object
top.errorlod
List genotypes with large error LOD scores
scanoneboot
Bootstrap to get interval estimate of QTL location
mqmpermutation
Estimate QTL LOD score significance using permutations or simulations
mqmplot.multitrait
Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes
pull.argmaxgeno
Pull out the results of the Viterbi algorithm from a cross
mqmscan
Genome scan with a multiple QTL model (MQM)
map10
An example genetic map
groupclusteredheatmap
Retrieving groups of traits after clustering
nphe
Determine the number of phenotypes QTL experiment
subset.scanoneperm
Subsetting permutation test results
badorder
An intercross with misplaced markers
plot.qtl
Plot QTL locations
inferredpartitions
Identify inferred partitions in mapping QTL to a phylogenetic tree
totmar
Determine the total number of markers
fitqtl
Fit a multiple-QTL model
qtlversion
Installed version of R/qtl
phenames
Pull out the phenotypes names from a cross
sim.geno
Simulate genotypes given observed marker data
max.scantwo
Maximum peak in two-dimensional genome scan
replaceqtl
Replace a QTL in a qtl object with a different position
plotRF
Plot recombination fractions
mqmplot.directedqtl
Plot LOD*Effect curves of a multiple-QTL model
summary.scanoneperm
LOD thresholds from scanone permutation results
plot.scanoneperm
Plot permutation results for a single-QTL genome scan
pull.pheno
Pull out phenotype data from a cross
summaryMap
Print summary of a genetic map
stepwiseqtl
Stepwise selection for multiple QTL
readMWril
Read data for 4- or 8-way RIL
ripple
Compare marker orders
tryallpositions
Test all possible positions for a marker
subset.map
Subsetting chromosomes for a genetic map
find.markerpos
Find position of a marker
scanone
Genome scan with a single QTL model
refineqtl
Refine the positions of QTL
fitstahl
Fit Stahl interference model
simFounderSnps
Simulate founder SNPs for a multiple-strain RIL
simPhyloQTL
Simulate a set of intercrosses for a single diallelic QTL
plotGeno
Plot observed genotypes, flagging likely errors
scantwopermhk
Permutation test for 2d genome scan by Haley-Knott regression
typingGap
Maximum distance between genotyped markers
mqmscanall
Parallelized MQM on multiple phenotypes in a cross object
pickMarkerSubset
Identify the largest subset of markers that are some distance apart
plotMissing
Plot grid of missing genotypes
nchr
Determine the number of chromosomes
pull.geno
Pull out the genotype data from a cross
compareorder
Compare two orderings of markers on a chromosome
scantwo
Two-dimensional genome scan with a two-QTL model
simulatemissingdata
Simulates missing genotype data
switch.order
Switch the order of markers on a chromosome
scanonevar.meanperm
Permutation test for mean effect in scanonevar
subset.scantwoperm
Subsetting two-dimensional permutation test results
summary.cross
Print summary of QTL experiment
summary.fitqtl
Summary of fit of qtl model
switchAlleles
Switch alleles at selected markers
xaxisloc.scanone
Get x-axis locations in scanone plot
inferFounderHap
Crude reconstruction of founder haplotypes in multi-parent RIL
multitrait
Example Cross object from R/QTL with multiple traits
mqmgetmodel
Retrieve the QTL model used in mapping from the results of an MQM scan
mqmplot.clusteredheatmap
Plot clustered heatmap of MQM scan on multiple phenotypes
plotLodProfile
Plot 1-d LOD profiles for a multiple QTL model
scanonevar.varperm
Permutation test for variance effect in scanonevar