Man pages for kbroman/qtl
Tools for Analyzing QTL Experiments

add.cim.covarIndicate marker covariates from composite interval mapping
addcovarintAdd QTL x covariate interaction to a multiple-QTL model
addintAdd pairwise interaction to a multiple-QTL model
addloctocrossAdd phenotype location into a cross object
addmarkerAdd a marker to a cross
addpairScan for an additional pair of QTL in a multiple-QTL model
addqtlScan for an additional QTL in a multiple-QTL model
add.thresholdAdd significance threshold to plot
addtoqtlAdd to a qtl object
allchrsplitsTest all possible splits of a chromosome into two pieces
argmax.genoReconstruct underlying genotypes
arithscanArithmetic operators for scanone and scantwo results
arithscanpermArithmetic Operators for permutation results
a.starting.pointIntroductory comments on R/qtl
badorderAn intercross with misplaced markers
bayesintBayesian credible interval
bristle3Data on bristle number in Drosophila
bristleXData on bristle number in Drosophila
calc.errorlodIdentify likely genotyping errors
calc.genoprobCalculate conditional genotype probabilities
calc.penaltiesCalculate LOD penalties
cbind.scanonepermCombine columns from multiple scanone permutation results
cbind.scantwopermCombine scantwo permutations by column
c.crossCombine data for QTL experiments
checkAllelesIdentify markers with switched alleles
chrlenChromosome lengths in QTL experiment
chrnamesPull out the chromosome names from a cross
cimComposite interval mapping
clean.crossRemove derived data
cleanGenoDelete genotypes that are possibly in error
clean.scantwoClean up scantwo output
comparecrossesCompare two cross objects
comparegenoCompare individuals' genotype data
compareorderCompare two orderings of markers on a chromosome
condense.scantwoCondense the output from a 2-d genome scan
convert2riselfConvert a cross to RIL by selfing
convert2risibConvert a cross to RIL by sib mating
convert2saConvert a sex-specific map to a sex-averaged one
convert.mapChange map function for a genetic map
convert.scanoneConvert output from scanone for R/qtl version 0.98
convert.scantwoConvert output from scantwo for R/qtl version 1.03 and...
countXOCount number of obligate crossovers for each individual
c.scanoneCombine columns from multiple scanone results
c.scanonepermCombine data from scanone permutations
c.scantwoCombine columns from multiple scantwo results
c.scantwopermCombine data from scantwo permutations
drop.dupmarkersDrop duplicate markers
dropfromqtlDrop a QTL from a qtl object
drop.markersDrop a set of markers
drop.nullmarkersDrop markers without any genotype data
droponemarkerDrop one marker at a time and determine effect on genetic map
effectplotPlot phenotype means against genotypes at one or two markers
effectscanPlot estimated QTL effects across the whole genome
est.mapEstimate genetic maps
est.rfEstimate pairwise recombination fractions
fake.4waySimulated data for a 4-way cross
fake.bcSimulated data for a backcross
fake.f2Simulated data for an F2 intercross
fill.genoFill holes in genotype data
findDupMarkersFind markers with identical genotype data
find.flankingFind flanking markers for a specified position
find.markerFind marker closest to a specified position
findmarkerindexDetermine the numeric index for a marker
find.markerposFind position of a marker
find.phenoFind column number for a particular phenotype
find.pseudomarkerFind the pseudomarker closest to a specified position
fitqtlFit a multiple-QTL model
fitstahlFit Stahl interference model
flip.orderFlip the orders of markers on a set of chromosomes
formLinkageGroupsPartition markers into linkage groups
formMarkerCovarCreate matrix of marker covariates for QTL analysis
geno.crosstabCreate table of two-locus genotypes
geno.imagePlot grid of genotype data
geno.tableCreate table of genotype distributions
getidPull out the individual identifiers from a cross
groupclusteredheatmapRetrieving groups of traits after clustering
hyperData on hypertension
inferFounderHapCrude reconstruction of founder haplotypes in multi-parent...
inferredpartitionsIdentify inferred partitions in mapping QTL to a phylogenetic...
interpPositionsInterpolate positions from one map to another
jittermapJitter marker positions in a genetic map
listeriaData on Listeria monocytogenes susceptibility
locateXOEstimate locations of crossovers
locationsGenetic locations of traits for the multitrait dataset
lodintLOD support interval
makeqtlMake a qtl object
map10An example genetic map
map2tableConvert genetic map from list to table.
mapthisSimulated data for illustrating genetic map construction
markerlrtGeneral likelihood ratio test for association between marker...
markernamesPull out the marker names from a cross
max.scanoneMaximum peak in genome scan
max.scanPhyloQTLMaximum peak in genome scan to map a QTL to a phylogenetic...
max.scantwoMaximum peak in two-dimensional genome scan
movemarkerMove a marker to a new chromosome
MQMIntroduction to Multiple QTL Model (MQM) mapping
mqmaugmentMQM augmentation
mqmautocofactorsAutomatic setting of cofactors, taking marker density into...
mqmextractmarkersMQM marker extraction
mqmfind.markerFetch significant markers after permutation analysis
mqmgetmodelRetrieve the QTL model used in mapping from the results of an...
mqmpermutationEstimate QTL LOD score significance using permutations or...
mqmplotcircleCircular genome plot for MQM
mqmplotcistranscis-trans plot
mqmplotclusteredheatmapPlot clustered heatmap of MQM scan on multiple phenotypes
mqmplotcofactorsPlot cofactors on the genetic map
mqmplotdirectedqtlPlot LOD*Effect curves of a multiple-QTL model
mqmplotheatmapHeatmap of a genome of MQM scan on multiple phenotypes
mqmplotmultitraitPlot the results from a genomescan using a multiple-QTL model...
mqmplotpermutationsPlot results from mqmpermutation
mqmplotsingletraitPlot LOD curves of a multiple-QTL model
mqmprocesspermutationConvert mqmmulti objects into a scanoneperm object
mqmscanGenome scan with a multiple QTL model (MQM)
mqmscanallParallelized MQM on multiple phenotypes in a cross object
mqmscanfdrEstimate FDR for multiple trait QTL analysis
mqmsetcofactorsSet cofactors at fixed intervals, to be used with MQM
mqmtestnormalShapiro normality test used for MQM
multitraitExample Cross object from R/QTL with multiple traits
nchrDetermine the number of chromosomes
nindDetermine the number of individuals QTL experiment
nmarDetermine the numbers of markers on each chromosome
nmissingNumber of missing genotypes
npheDetermine the number of phenotypes QTL experiment
nqrankTransform a vector of quantitative values to the...
nqtlDetermine the number of QTL in a QTL object
ntypedNumber of genotypes
nullmarkersIdentify markers without any genotype data
orderMarkersFind an initial order for markers within chromosomes
phenamesPull out the phenotypes names from a cross
pickMarkerSubsetIdentify the largest subset of markers that are some distance...
plot.crossPlot various features of a cross object
plot.errorlodPlot grid of error LOD values
plot.genoPlot observed genotypes, flagging likely errors
plot.infoPlot the proportion of missing genotype information
plotLodProfilePlot 1-d LOD profiles for a multiple QTL model
plot.mapPlot genetic map
plot.missingPlot grid of missing genotypes
plotModelPlot a QTL model
plot.phenoPlot a phenotype distribution
plot.pxgPlot phenotypes versus marker genotypes
plot.qtlPlot QTL locations
plot.rfPlot recombination fractions
plot.rfmatrixPlot recombination fractions or LOD scores for a single...
plot.scanonePlot LOD curves
plot.scanonebootPlot results of bootstrap for QTL position
plot.scanonepermPlot permutation results for a single-QTL genome scan
plot.scanPhyloQTLPlot LOD curves from single-QTL scan to map QTL to a...
plot.scantwoPlot LOD scores for a two-dimensional genome scan
plot.scantwopermPlot permutation results for a 2d, 2-QTL genome scan
pull.argmaxgenoPull out the results of the Viterbi algorithm from a cross
pull.drawsPull out the genotype imputations from a cross
pull.genoPull out the genotype data from a cross
pull.genoprobPull out the genotype probabilities from a cross
pull.mapPull out the genetic map from a cross
pull.markersDrop all but a selected set of markers
pull.phenoPull out phenotype data from a cross
pull.rfPull out recombination fractions or LOD scores from a cross...
qtl-internalInternal qtl functions
qtlversionInstalled version of R/qtl
read.crossRead data for a QTL experiment
readMWrilRead data for 4- or 8-way RIL
reduce2gridReduce to a grid of pseudomarkers.
refineqtlRefine the positions of QTL
reorderqtlReorder the QTL in a qtl object
replace.mapReplace the genetic map of a cross
replacemap.scanoneReplace the genetic map in QTL mapping results with an...
replacemap.scantwoReplace the genetic map in QTL mapping results with an...
replaceqtlReplace a QTL in a qtl object with a different position
rescalemapRescale genetic maps
rippleCompare marker orders
scanoneGenome scan with a single QTL model
scanonebootBootstrap to get interval estimate of QTL location
scanonevarGenome scan for QTL affecting mean and/or variance
scanonevar.meanpermPermutation test for mean effect in scanonevar
scanonevar.varpermPermutation test for variance effect in scanonevar
scanPhyloQTLSingle-QTL genome scan to map QTL to a phylogenetic tree
scanqtlGeneral QTL scan
scantwoTwo-dimensional genome scan with a two-QTL model
scantwopermhkPermutation test for 2d genome scan by Haley-Knott regression
shiftmapShift starting points in genetic maps
sim.crossSimulate a QTL experiment
simFounderSnpsSimulate founder SNPs for a multiple-strain RIL
sim.genoSimulate genotypes given observed marker data
sim.mapSimulate a genetic map
simPhyloQTLSimulate a set of intercrosses for a single diallelic QTL
simulateMissingDataSimulates missing genotype data
stepwiseqtlStepwise selection for multiple QTL
strip.partialsStrip partially informative genotypes
subset.crossSubsetting data for QTL experiment
subset.mapSubsetting chromosomes for a genetic map
subset.scanoneSubsetting the results of a genome scan
subset.scanonepermSubsetting permutation test results
subset.scantwoSubsetting the results of a 2-d genome scan
subset.scantwopermSubsetting two-dimensional permutation test results
summary.crossPrint summary of QTL experiment
summary.fitqtlSummary of fit of qtl model
summary.mapPrint summary of a genetic map
summary.qtlPrint summary of a QTL object
summary.ripplePrint summary of ripple results
summary.scanoneSummarize the results of a genome scans
summary.scanonebootBootstrap confidence interval for QTL location
summary.scanonepermLOD thresholds from scanone permutation results
summary.scanPhyloQTLSummarize the results a genome scan to map a QTL to a...
summary.scantwoSummarize the results of a two-dimensional genome scan
summary.scantwo.oldSummarize the results of a two-dimensional genome scan
summary.scantwopermLOD thresholds from scantwo permutation results
switchAllelesSwitch alleles at selected markers
switch.orderSwitch the order of markers on a chromosome
table2mapConvert a table of marker positions to a map object.
top.errorlodList genotypes with large error LOD scores
totmarDetermine the total number of markers
transformPhenoTransformation of the phenotypes in a cross object
tryallpositionsTest all possible positions for a marker
typingGapMaximum distance between genotyped markers
write.crossWrite data for a QTL experiment to a file
xaxisloc.scanoneGet x-axis locations in scanone plot
kbroman/qtl documentation built on Jan. 14, 2019, 5:20 a.m.