# Tools for Analyzing QTL Experiments

## Documentation for package ‘qtl’ version 1.74

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I J L M N O P Q R S T W X misc

qtl-package | Introductory comments on R/qtl

## -- A --

add.cim.covar | Indicate marker covariates from composite interval mapping
add.threshold | Add significance threshold to plot
addcovarint | Add QTL x covariate interaction to a multiple-QTL model
addint | Add pairwise interaction to a multiple-QTL model
addloctocross | Add phenotype location into a cross object
addmarker | Add a marker to a cross
addpair | Scan for an additional pair of QTL in a multiple-QTL model
addqtl | Scan for an additional QTL in a multiple-QTL model
addtoqtl | Add to a qtl object
allchrsplits | Test all possible splits of a chromosome into two pieces
argmax.geno | Reconstruct underlying genotypes

## -- B --

badorder | An intercross with misplaced markers
bayesint | Bayesian credible interval
bristle3 | Data on bristle number in Drosophila
bristleX | Data on bristle number in Drosophila

## -- C --

c.cross | Combine data for QTL experiments
c.scanone | Combine columns from multiple scanone results
c.scanoneperm | Combine data from scanone permutations
c.scantwo | Combine columns from multiple scantwo results
c.scantwoperm | Combine data from scantwo permutations
calc.errorlod | Identify likely genotyping errors
calc.genoprob | Calculate conditional genotype probabilities
calc.penalties | Calculate LOD penalties
cbind.scanone | Combine columns from multiple scanone results
cbind.scanoneperm | Combine columns from multiple scanone permutation results
cbind.scantwo | Combine columns from multiple scantwo results
cbind.scantwoperm | Combine scantwo permutations by column
checkAlleles | Identify markers with switched alleles
chrlen | Chromosome lengths in QTL experiment
chrnames | Pull out the chromosome names from a cross
cim | Composite interval mapping
clean.cross | Remove derived data
clean.scantwo | Clean up scantwo output
cleanGeno | Delete genotypes that are possibly in error
comparecrosses | Compare two cross objects
comparegeno | Compare individuals' genotype data
compareorder | Compare two orderings of markers on a chromosome
condense.scantwo | Condense the output from a 2-d genome scan
convert.map | Change map function for a genetic map
convert.scanone | Convert output from scanone for R/qtl version 0.98
convert.scantwo | Convert output from scantwo for R/qtl version 1.03 and earlier
convert2riself | Convert a cross to RIL by selfing
convert2risib | Convert a cross to RIL by sib mating
convert2sa | Convert a sex-specific map to a sex-averaged one
countXO | Count number of obligate crossovers for each individual

## -- D --

drop.dupmarkers | Drop duplicate markers
drop.markers | Drop a set of markers
drop.nullmarkers | Drop markers without any genotype data
dropfromqtl | Drop a QTL from a qtl object
droponemarker | Drop one marker at a time and determine effect on genetic map

## -- E --

effectplot | Plot phenotype means against genotypes at one or two markers
effectscan | Plot estimated QTL effects across the whole genome
est.map | Estimate genetic maps
est.rf | Estimate pairwise recombination fractions

## -- F --

fake.4way | Simulated data for a 4-way cross
fake.bc | Simulated data for a backcross
fake.f2 | Simulated data for an F2 intercross
fill.geno | Fill holes in genotype data
find.flanking | Find flanking markers for a specified position
find.marker | Find marker closest to a specified position
find.markerindex | Determine the numeric index for a marker
find.markerpos | Find position of a marker
find.pheno | Find column number for a particular phenotype
find.pseudomarker | Find the pseudomarker closest to a specified position
findDupMarkers | Find markers with identical genotype data
find_large_intervals | Find large intervals in a map
fitqtl | Fit a multiple-QTL model
fitstahl | Fit Stahl interference model
flip.order | Flip the orders of markers on a set of chromosomes
formLinkageGroups | Partition markers into linkage groups
formMarkerCovar | Create matrix of marker covariates for QTL analysis

## -- G --

geno.crosstab | Create table of two-locus genotypes
geno.image | Plot grid of genotype data
geno.table | Create table of genotype distributions
getid | Pull out the individual identifiers from a cross
groupclusteredheatmap | Retrieving groups of traits after clustering

## -- H --

hyper | Data on hypertension

## -- I --

inferFounderHap | Crude reconstruction of founder haplotypes in multi-parent RIL
inferredpartitions | Identify inferred partitions in mapping QTL to a phylogenetic tree
interpPositions | Interpolate positions from one map to another

## -- J --

jittermap | Jitter marker positions in a genetic map

## -- L --

listeria | Data on Listeria monocytogenes susceptibility
locateXO | Estimate locations of crossovers
locations | Genetic locations of traits for the multitrait dataset
lodint | LOD support interval

## -- M --

makeqtl | Make a qtl object
map10 | An example genetic map
map2table | Convert genetic map from list to table.
mapthis | Simulated data for illustrating genetic map construction
markerlrt | General likelihood ratio test for association between marker pairs
markernames | Pull out the marker names from a cross
max.scanone | Maximum peak in genome scan
max.scanPhyloQTL | Maximum peak in genome scan to map a QTL to a phylogenetic tree
max.scantwo | Maximum peak in two-dimensional genome scan
movemarker | Move a marker to a new chromosome
MQM | Introduction to Multiple QTL Model (MQM) mapping
mqmaugment | MQM augmentation
mqmautocofactors | Automatic setting of cofactors, taking marker density into account
mqmextractmarkers | MQM marker extraction
mqmfind.marker | Fetch significant markers after permutation analysis
mqmgetmodel | Retrieve the QTL model used in mapping from the results of an MQM scan
mqmpermutation | Estimate QTL LOD score significance using permutations or simulations
mqmplot.circle | Circular genome plot for MQM
mqmplot.cistrans | cis-trans plot
mqmplot.clusteredheatmap | Plot clustered heatmap of MQM scan on multiple phenotypes
mqmplot.cofactors | Plot cofactors on the genetic map
mqmplot.directedqtl | Plot LOD*Effect curves of a multiple-QTL model
mqmplot.heatmap | Heatmap of a genome of MQM scan on multiple phenotypes
mqmplot.multitrait | Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes
mqmplot.permutations | Plot results from mqmpermutation
mqmplot.singletrait | Plot LOD curves of a multiple-QTL model
mqmprocesspermutation | Convert mqmmulti objects into a scanoneperm object
mqmscan | Genome scan with a multiple QTL model (MQM)
mqmscanall | Parallelized MQM on multiple phenotypes in a cross object
mqmscanfdr | Estimate FDR for multiple trait QTL analysis
mqmsetcofactors | Set cofactors at fixed intervals, to be used with MQM
mqmtestnormal | Shapiro normality test used for MQM
multitrait | Example Cross object from R/QTL with multiple traits

## -- N --

nchr | Determine the number of chromosomes
nind | Determine the number of individuals QTL experiment
nmar | Determine the numbers of markers on each chromosome
nmissing | Number of missing genotypes
nphe | Determine the number of phenotypes QTL experiment
nqrank | Transform a vector of quantitative values to the corresponding normal quantiles
nqtl | Determine the number of QTL in a QTL object
ntyped | Number of genotypes
nullmarkers | Identify markers without any genotype data

## -- O --

orderMarkers | Find an initial order for markers within chromosomes

## -- P --

phenames | Pull out the phenotypes names from a cross
pickMarkerSubset | Identify the largest subset of markers that are some distance apart
plot.comparegeno | Plot genotype comparison
plot.cross | Plot various features of a cross object
plot.map | Plot genetic map
plot.qtl | Plot QTL locations
plot.rfmatrix | Plot recombination fractions or LOD scores for a single marker
plot.scanone | Plot LOD curves
plot.scanoneboot | Plot results of bootstrap for QTL position
plot.scanoneperm | Plot permutation results for a single-QTL genome scan
plot.scanPhyloQTL | Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree
plot.scantwo | Plot LOD scores for a two-dimensional genome scan
plot.scantwoperm | Plot permutation results for a 2d, 2-QTL genome scan
plotErrorlod | Plot grid of error LOD values
plotGeno | Plot observed genotypes, flagging likely errors
plotInfo | Plot the proportion of missing genotype information
plotLodProfile | Plot 1-d LOD profiles for a multiple QTL model
plotMap | Plot genetic map
plotMissing | Plot grid of missing genotypes
plotModel | Plot a QTL model
plotPheno | Plot a phenotype distribution
plotPXG | Plot phenotypes versus marker genotypes
plotRF | Plot recombination fractions
pull.argmaxgeno | Pull out the results of the Viterbi algorithm from a cross
pull.draws | Pull out the genotype imputations from a cross
pull.geno | Pull out the genotype data from a cross
pull.genoprob | Pull out the genotype probabilities from a cross
pull.map | Pull out the genetic map from a cross
pull.markers | Drop all but a selected set of markers
pull.pheno | Pull out phenotype data from a cross
pull.rf | Pull out recombination fractions or LOD scores from a cross object

## -- Q --

qtlversion | Installed version of R/qtl

## -- R --

rbind.scanoneperm | Combine data from scanone permutations
rbind.scantwoperm | Combine data from scantwo permutations
read.cross | Read data for a QTL experiment
readMWril | Read data for 4- or 8-way RIL
reduce2grid | Reduce to a grid of pseudomarkers.
refineqtl | Refine the positions of QTL
reorderqtl | Reorder the QTL in a qtl object
replace.map | Replace the genetic map of a cross
replacemap.cross | Replace the genetic map of a cross
replacemap.scanone | Replace the genetic map in QTL mapping results with an alternate map
replacemap.scantwo | Replace the genetic map in QTL mapping results with an alternate map
replaceqtl | Replace a QTL in a qtl object with a different position
rescalemap | Rescale genetic maps
ripple | Compare marker orders

## -- S --

scanone | Genome scan with a single QTL model
scanoneboot | Bootstrap to get interval estimate of QTL location
scanonevar | Genome scan for QTL affecting mean and/or variance
scanonevar.meanperm | Permutation test for mean effect in scanonevar
scanonevar.varperm | Permutation test for variance effect in scanonevar
scanPhyloQTL | Single-QTL genome scan to map QTL to a phylogenetic tree
scanqtl | General QTL scan
scantwo | Two-dimensional genome scan with a two-QTL model
scantwopermhk | Permutation test for 2d genome scan by Haley-Knott regression
shiftmap | Shift starting points in genetic maps
sim.cross | Simulate a QTL experiment
sim.geno | Simulate genotypes given observed marker data
sim.map | Simulate a genetic map
simFounderSnps | Simulate founder SNPs for a multiple-strain RIL
simPhyloQTL | Simulate a set of intercrosses for a single diallelic QTL
simulatemissingdata | Simulates missing genotype data
stepwiseqtl | Stepwise selection for multiple QTL
strip.partials | Strip partially informative genotypes
subset.cross | Subsetting data for QTL experiment
subset.map | Subsetting chromosomes for a genetic map
subset.scanone | Subsetting the results of a genome scan
subset.scanoneperm | Subsetting permutation test results
subset.scantwo | Subsetting the results of a 2-d genome scan
subset.scantwoperm | Subsetting two-dimensional permutation test results
summary.comparegeno | Print pairs of individuals with similar genotype data.
summary.cross | Print summary of QTL experiment
summary.fitqtl | Summary of fit of qtl model
summary.map | Print summary of a genetic map
summary.qtl | Print summary of a QTL object
summary.ripple | Print summary of ripple results
summary.scanone | Summarize the results of a genome scans
summary.scanoneboot | Bootstrap confidence interval for QTL location
summary.scanoneperm | LOD thresholds from scanone permutation results
summary.scanPhyloQTL | Summarize the results a genome scan to map a QTL to a phylogenetic tree
summary.scantwo | Summarize the results of a two-dimensional genome scan
summary.scantwoperm | LOD thresholds from scantwo permutation results
summaryMap | Print summary of a genetic map
summaryScantwoOld | Summarize the results of a two-dimensional genome scan
switch.order | Switch the order of markers on a chromosome
switchAlleles | Switch alleles at selected markers

## -- T --

table2map | Convert a table of marker positions to a map object.
top.errorlod | List genotypes with large error LOD scores
totmar | Determine the total number of markers
transformPheno | Transformation of the phenotypes in a cross object
tryallpositions | Test all possible positions for a marker
typingGap | Maximum distance between genotyped markers

## -- W --

write.cross | Write data for a QTL experiment to a file

## -- X --

xaxisloc.scanone | Get x-axis locations in scanone plot

## -- misc --

+.scanone | Arithmetic operators for scanone and scantwo results
+.scanoneperm | Arithmetic Operators for permutation results
+.scantwo | Arithmetic operators for scanone and scantwo results
+.scantwoperm | Arithmetic Operators for permutation results
-.scanone | Arithmetic operators for scanone and scantwo results
-.scanoneperm | Arithmetic Operators for permutation results
-.scantwo | Arithmetic operators for scanone and scantwo results
-.scantwoperm | Arithmetic Operators for permutation results
[.cross | Subsetting data for QTL experiment
[.map | Subsetting chromosomes for a genetic map
[.scanoneperm | Subsetting permutation test results
[.scantwoperm | Subsetting two-dimensional permutation test results