Tools for Analyzing QTL Experiments


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Documentation for package ‘qtl’ version 1.50

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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