/usr/lib/R/site-library/qtl/INDEX is in r-cran-qtl 1.27-10-1.
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results
+.scanoneperm Arithmetic Operators for permutation results
MQM Introduction to Multiple QTL Model (MQM)
mapping
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
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
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.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.scanoneperm Combine columns from multiple scanone
permutation results
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
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
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
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
fitqtl Fit a multiple-QTL model
fitstahl Fit Stahl interference model
formLinkageGroups Partition markers into linkage groups
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
hyper Data on hypertension
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
jittermap Jitter marker positions in a genetic map
listeria Data on Listeria monocytogenes susceptibility
locateXO Estimate locations of crossovers
locations Genetic locations of traits for the multitrait
dataset
lodint LOD support interval
makeqtl Make a qtl object
map10 An example genetic map
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.scanPhyloQTL Maximum peak in genome scan to map a QTL to a
phylogenetic tree
max.scanone Maximum peak in genome scan
max.scantwo Maximum peak in two-dimensional genome scan
movemarker Move a marker to a new chromosome
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
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
ntyped Number of genotypes
nullmarkers Identify markers without any genotype data
orderMarkers Find an initial order for markers within
chromosomes
phenames Pull out the phenotypes names from a cross
pickMarkerSubset Identify the largest subset of markers that are
some distance apart
plot.cross Plot various features of a cross object
plot.qtl Plot QTL locations
plot.rfmatrix Plot recombination fractions or LOD scores for
a single marker
plot.scanPhyloQTL Plot LOD curves from single-QTL scan to map QTL
to a phylogenetic tree
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.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
plotPXG Plot phenotypes versus marker genotypes
plotPheno Plot a phenotype distribution
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
qtl-package Introductory comments on R/qtl
qtlversion Installed version of R/qtl
read.cross Read data for a QTL experiment
readMWril Read data for 4- or 8-way RIL
refineqtl Refine the positions of QTL
reorderqtl Reorder the QTL in a qtl object
replace.map 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
scanPhyloQTL Single-QTL genome scan to map QTL to a
phylogenetic tree
scanone Genome scan with a single QTL model
scanoneboot Bootstrap to get interval estimate of QTL
location
scanqtl General QTL scan
scantwo Two-dimensional genome scan with a two-QTL
model
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.cross Print summary of QTL experiment
summary.fitqtl Summary of fit of qtl model
summary.qtl Print summary of a QTL object
summary.ripple Print summary of ripple results
summary.scanPhyloQTL Summarize the results a genome scan to map a
QTL to a phylogenetic tree
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.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
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
write.cross Write data for a QTL experiment to a file
xaxisloc.scanone Get x-axis locations in scanone plot
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