qtl: Tools for Analyzing QTL Experiments

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Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.

Author
Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Date of publication
2016-11-05 08:59:40
Maintainer
Karl W Broman <kbroman@biostat.wisc.edu>
License
GPL-3
Version
1.40-8
URLs

View on CRAN

Man pages

add.cim.covar
Indicate marker covariates from composite interval mapping
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
add.threshold
Add significance threshold to plot
addtoqtl
Add to a qtl object
allchrsplits
Test all possible splits of a chromosome into two pieces
argmax.geno
Reconstruct underlying genotypes
arithscan
Arithmetic operators for scanone and scantwo results
arithscanperm
Arithmetic Operators for permutation results
a.starting.point
Introductory comments on R/qtl
badorder
An intercross with misplaced markers
bayesint
Bayesian credible interval
bristle3
Data on bristle number in Drosophila
bristleX
Data on bristle number in Drosophila
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
cbind.scantwoperm
Combine scantwo permutations by column
c.cross
Combine data for QTL experiments
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
cleanGeno
Delete genotypes that are possibly in error
clean.scantwo
Clean up scantwo output
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
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
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...
countXO
Count number of obligate crossovers for each individual
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
drop.dupmarkers
Drop duplicate markers
dropfromqtl
Drop a QTL from a qtl object
drop.markers
Drop a set of markers
drop.nullmarkers
Drop markers without any genotype data
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
findDupMarkers
Find markers with identical genotype data
find.flanking
Find flanking markers for a specified position
find.marker
Find marker closest to a specified position
findmarkerindex
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
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
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...
inferredpartitions
Identify inferred partitions in mapping QTL to a phylogenetic...
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
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...
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...
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...
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...
mqmpermutation
Estimate QTL LOD score significance using permutations or...
mqmplotcircle
Circular genome plot for MQM
mqmplotcistrans
cis-trans plot
mqmplotclusteredheatmap
Plot clustered heatmap of MQM scan on multiple phenotypes
mqmplotcofactors
Plot cofactors on the genetic map
mqmplotdirectedqtl
Plot LOD*Effect curves of a multiple-QTL model
mqmplotheatmap
Heatmap of a genome of MQM scan on multiple phenotypes
mqmplotmultitrait
Plot the results from a genomescan using a multiple-QTL model...
mqmplotpermutations
Plot results from mqmpermutation
mqmplotsingletrait
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...
nqtl
Determine the number of QTL in a QTL object
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...
plot.cross
Plot various features of a cross object
plot.errorlod
Plot grid of error LOD values
plot.geno
Plot observed genotypes, flagging likely errors
plot.info
Plot the proportion of missing genotype information
plotLodProfile
Plot 1-d LOD profiles for a multiple QTL model
plot.map
Plot genetic map
plot.missing
Plot grid of missing genotypes
plotModel
Plot a QTL model
plot.pheno
Plot a phenotype distribution
plot.pxg
Plot phenotypes versus marker genotypes
plot.qtl
Plot QTL locations
plot.rf
Plot recombination fractions
plot.rfmatrix
Plot recombination fractions or LOD scores for a single...
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...
plot.scantwo
Plot LOD scores for a two-dimensional genome scan
plot.scantwoperm
Plot permutation results for a 2d, 2-QTL genome scan
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...
qtl-internal
Internal qtl functions
qtlversion
Installed version of R/qtl
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.scanone
Replace the genetic map in QTL mapping results with an...
replacemap.scantwo
Replace the genetic map in QTL mapping results with an...
replaceqtl
Replace a QTL in a qtl object with a different position
rescalemap
Rescale genetic maps
ripple
Compare marker orders
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
simFounderSnps
Simulate founder SNPs for a multiple-strain RIL
sim.geno
Simulate genotypes given observed marker data
sim.map
Simulate a genetic map
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.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...
summary.scantwo
Summarize the results of a two-dimensional genome scan
summary.scantwo.old
Summarize the results of a two-dimensional genome scan
summary.scantwoperm
LOD thresholds from scantwo permutation results
switchAlleles
Switch alleles at selected markers
switch.order
Switch the order of markers on a chromosome
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
write.cross
Write data for a QTL experiment to a file
xaxisloc.scanone
Get x-axis locations in scanone plot

Files in this package

qtl
qtl/inst
qtl/inst/BUGS.txt
qtl/inst/CITATION
qtl/inst/TODO.txt
qtl/inst/STATUS.txt
qtl/inst/LICENSE.txt
qtl/inst/MQM-TODO.txt
qtl/inst/README.md
qtl/inst/INSTALL_ME.txt
qtl/inst/doc
qtl/inst/doc/geneticmaps.pdf
qtl/inst/doc/Sources
qtl/inst/doc/Sources/new_multiqtl.Rnw
qtl/inst/doc/Sources/rqtltour.tex
qtl/inst/doc/Sources/rqtltour2.tex
qtl/inst/doc/Sources/new_summary_scantwo.Rnw
qtl/inst/doc/Sources/geneticmaps.Rnw
qtl/inst/doc/Sources/new_summary_scanone.Rnw
qtl/inst/doc/Sources/MQM
qtl/inst/doc/Sources/MQM/sweaveit.sh
qtl/inst/doc/Sources/MQM/MQM-tour.Rnw
qtl/inst/doc/Sources/MQM/mqm
qtl/inst/doc/Sources/MQM/mqm/description.txt
qtl/inst/doc/Sources/MQM/mqm/standard_references.txt
qtl/inst/doc/Sources/MQM/mqm/standard_example.txt
qtl/inst/doc/Sources/MQM/mqm/standard_seealso.txt
qtl/inst/doc/Sources/MQM/mqm/limitations.txt
qtl/inst/doc/Sources/MQM/mqm/advantages_latex.txt
qtl/inst/doc/Sources/MQM/mqm/advantages_Rd.txt
qtl/inst/doc/Sources/MQM/mqm/significance_references.txt
qtl/inst/doc/Sources/MQM/mqm/parallelisation_references.txt
qtl/inst/doc/Sources/MQM/SweaveIt.R
qtl/inst/doc/Sources/MQM/sweaveit.bat
qtl/inst/doc/bcsft.pdf
qtl/inst/doc/new_multiqtl.R
qtl/inst/doc/rqtltour2.pdf
qtl/inst/doc/rqtltour2.R
qtl/inst/doc/bcsft.Rnw
qtl/inst/doc/new_summary_scantwo.pdf
qtl/inst/doc/geneticmaps.R
qtl/inst/doc/new_multiqtl.pdf
qtl/inst/doc/bcsft.R
qtl/inst/doc/new_summary_scanone.R
qtl/inst/doc/rqtltour.R
qtl/inst/doc/rqtltour.pdf
qtl/inst/doc/new_summary_scantwo.R
qtl/inst/doc/new_summary_scanone.pdf
qtl/inst/contrib
qtl/inst/contrib/biolib
qtl/inst/contrib/biolib/CMakeLists.txt
qtl/inst/contrib/biolib/README
qtl/inst/contrib/scripts
qtl/inst/contrib/scripts/check_rqtl.sh
qtl/inst/contrib/scripts/cleanup.sh
qtl/inst/contrib/scripts/repl_inputs.rb
qtl/inst/contrib/scripts/run_all_tests.sh
qtl/inst/contrib/scripts/update_header.rb
qtl/inst/contrib/scripts/install_rqtl.sh
qtl/inst/contrib/bin
qtl/inst/contrib/bin/mqmdebugout.cpp
qtl/inst/contrib/bin/CMakeLists.txt
qtl/inst/contrib/bin/wincompile.bat
qtl/inst/contrib/bin/scripts
qtl/inst/contrib/bin/scripts/cleanup.sh
qtl/inst/contrib/bin/scripts/profiler.sh
qtl/inst/contrib/bin/scripts/r.sh
qtl/inst/contrib/bin/scripts/regression_tests.sh
qtl/inst/contrib/bin/scripts/create-diff.sh
qtl/inst/contrib/bin/scripts/regression_tests_windows.bat
qtl/inst/contrib/bin/mqmmain.cpp
qtl/inst/contrib/bin/README
qtl/inst/contrib/bin/FindRLibs.cmake
qtl/inst/contrib/bin/regressiontests.bat
qtl/inst/contrib/bin/test
qtl/inst/contrib/bin/test/chridhyper.txt
qtl/inst/contrib/bin/test/filledgenohyper.txt
qtl/inst/contrib/bin/test/t12
qtl/inst/contrib/bin/test/t12/cofactors.txt
qtl/inst/contrib/bin/test/settingshyper.txt
qtl/inst/contrib/bin/test/phenohyper.txt
qtl/inst/contrib/bin/test/pheno.dat
qtl/inst/contrib/bin/test/genohyper.txt
qtl/inst/contrib/bin/test/t11
qtl/inst/contrib/bin/test/t11/cofactors.txt
qtl/inst/contrib/bin/test/regression
qtl/inst/contrib/bin/test/regression/t25out.txt
qtl/inst/contrib/bin/test/regression/t24out.txt
qtl/inst/contrib/bin/test/regression/t33out.txt
qtl/inst/contrib/bin/test/regression/t11out-test0.txt
qtl/inst/contrib/bin/test/regression/t32out.txt
qtl/inst/contrib/bin/test/regression/debugout_pbeta.txt
qtl/inst/contrib/bin/test/regression/debugout_dnorm.txt
qtl/inst/contrib/bin/test/regression/t34out.txt
qtl/inst/contrib/bin/test/regression/t12out.txt
qtl/inst/contrib/bin/test/regression/t31out.txt
qtl/inst/contrib/bin/test/regression/t21out.txt
qtl/inst/contrib/bin/test/regression/t13out.txt
qtl/inst/contrib/bin/test/regression/t23out.txt
qtl/inst/contrib/bin/test/regression/t22out.txt
qtl/inst/contrib/bin/test/regression/t11out.txt
qtl/inst/contrib/bin/test/cofactors.txt
qtl/inst/contrib/bin/test/std
qtl/inst/contrib/bin/test/std/settings3.txt
qtl/inst/contrib/bin/test/std/phenotypes2.txt
qtl/inst/contrib/bin/test/std/settings2.txt
qtl/inst/contrib/bin/test/std/genotypes3.txt
qtl/inst/contrib/bin/test/std/genotypes2.txt
qtl/inst/contrib/bin/test/std/genotypes1.txt
qtl/inst/contrib/bin/test/std/phenotypes3.txt
qtl/inst/contrib/bin/test/std/genotypes2m.txt
qtl/inst/contrib/bin/test/std/markers1.txt
qtl/inst/contrib/bin/test/std/settings1.txt
qtl/inst/contrib/bin/test/std/markers2.txt
qtl/inst/contrib/bin/test/std/genotypes3m.txt
qtl/inst/contrib/bin/test/std/markers3.txt
qtl/inst/contrib/bin/test/std/phenotypes1.txt
qtl/inst/contrib/bin/test/t33
qtl/inst/contrib/bin/test/t33/cofactors.txt
qtl/inst/contrib/bin/test/settings.dat
qtl/inst/contrib/bin/test/geno.dat
qtl/inst/contrib/bin/test/chrid.dat
qtl/inst/contrib/bin/test/t23
qtl/inst/contrib/bin/test/t23/cofactors.txt
qtl/inst/contrib/bin/test/markerpos.txt
qtl/inst/contrib/bin/test/t22
qtl/inst/contrib/bin/test/t22/cofactors.txt
qtl/inst/contrib/bin/test/markerposhyper.txt
qtl/inst/contrib/bin/rtest
qtl/inst/contrib/bin/rtest/test_mqm_hyper_prob.R
qtl/inst/contrib/bin/rtest/regression
qtl/inst/contrib/bin/rtest/regression/scanone_mr.rtest
qtl/inst/contrib/bin/rtest/regression/mqm_listeria1.rtest
qtl/inst/contrib/bin/rtest/test_mqm_listeria1.R
qtl/inst/contrib/bin/rtest/test_augmentation.R
qtl/inst/contrib/bin/rtest/test_scanone_mr.R
qtl/inst/sampledata
qtl/inst/sampledata/listeria_qc_cro.txt
qtl/inst/sampledata/listeria_qc_map.txt
qtl/inst/sampledata/listeria.csv
qtl/inst/sampledata/gen.txt
qtl/inst/sampledata/listeria_gen_rot.csv
qtl/inst/sampledata/listeria_phe_rot.csv
qtl/inst/sampledata/listeria_gen.csv
qtl/inst/sampledata/listeria_rot.csv
qtl/inst/sampledata/listeria.qtx
qtl/inst/sampledata/phe.txt
qtl/inst/sampledata/listeria_phe.csv
qtl/inst/sampledata/listeria_maps.txt
qtl/inst/sampledata/map.txt
qtl/inst/sampledata/README.txt
qtl/inst/sampledata/listeria_raw.txt
qtl/inst/sampledata/listeria_map.txt
qtl/tests
qtl/tests/listeria.csv
qtl/tests/gen.txt
qtl/tests/listeria.map
qtl/tests/test_scanonevar.R
qtl/tests/test_io.R
qtl/tests/testaugmentation.R
qtl/tests/test_tidyIO.Rout.save
qtl/tests/test_io.Rout.save
qtl/tests/phe.txt
qtl/tests/listeria2.map
qtl/tests/test_qtl.R
qtl/tests/test_mapqtl_io.R
qtl/tests/map.txt
qtl/tests/test_mapqtl_io.Rout.save
qtl/tests/testthat.R
qtl/tests/listeria2.csv
qtl/tests/testthat
qtl/tests/testthat/test-scantwoperm.R
qtl/tests/testthat/test-fliporder.R
qtl/tests/testthat/test-stepwiseqtl.R
qtl/tests/listeria.raw
qtl/tests/test_tidyIO.R
qtl/tests/test_scanonevar.Rout.save
qtl/src
qtl/src/hmm_main.h
qtl/src/mqmprob.cpp
qtl/src/mqmmixture.cpp
qtl/src/hmm_bcsft.h
qtl/src/fitqtl_imp_binary.h
qtl/src/fitqtl_imp_binary.c
qtl/src/Makevars
qtl/src/util.c
qtl/src/scanone_em.h
qtl/src/markerlrt.h
qtl/src/scantwo_binary_em.h
qtl/src/mqmdatatypes.cpp
qtl/src/mqmmapqtl.cpp
qtl/src/scantwo_imp.c
qtl/src/fitqtl_imp.c
qtl/src/hmm_ri4sib.h
qtl/src/simulate.c
qtl/src/hmm_util.c
qtl/src/hmm_bci.c
qtl/src/stahl_mf.c
qtl/src/inferFounderHap.h
qtl/src/scantwo_em.h
qtl/src/hmm_bgmagic16.c
qtl/src/hmm_ri8self.h
qtl/src/mqmeliminate.h
qtl/src/effectscan.c
qtl/src/scanone_mr.h
qtl/src/mqmeliminate.cpp
qtl/src/fitqtl_hk_binary.c
qtl/src/hmm_f2i.c
qtl/src/scanone_imp.c
qtl/src/ril48_reorg.h
qtl/src/hmm_ri8sib.c
qtl/src/vbscan.h
qtl/src/fill_geno_nodblXO.h
qtl/src/mqmregression.cpp
qtl/src/scanone_hk_binary.h
qtl/src/hmm_ri8sib.h
qtl/src/scantwopermhk.c
qtl/src/scanone_em_covar.h
qtl/src/hmm_f2i.h
qtl/src/discan_covar.h
qtl/src/hmm_bci.h
qtl/src/ripple.c
qtl/src/forwsel.h
qtl/src/simulate_ril.c
qtl/src/scanone_ehk.c
qtl/src/hmm_ri8selfIRIP1.h
qtl/src/mqmscan.h
qtl/src/mqmregression.h
qtl/src/scantwo_mr.c
qtl/src/standalone.h
qtl/src/test_bcsft.c
qtl/src/countXO.c
qtl/src/mqm.h
qtl/src/hmm_bcsft.c
qtl/src/mqmmapqtl.h
qtl/src/hmm_bc.c
qtl/src/hmm_util.h
qtl/src/scantwo_binary_hk.h
qtl/src/scanone_np.c
qtl/src/info.c
qtl/src/scanone_ehk.h
qtl/src/lapackutil.h
qtl/src/scanone_em.c
qtl/src/vbscan.c
qtl/src/simulate.h
qtl/src/scantwo_binary_em.c
qtl/src/util.h
qtl/src/summary_scantwo.h
qtl/src/scanone_mr.c
qtl/src/findDupMarkers_notexact.h
qtl/src/mqmprob.h
qtl/src/hmm_f2.c
qtl/src/mqmaugment.h
qtl/src/scantwopermhk.h
qtl/src/fitqtl_hk_binary.h
qtl/src/inferFounderHap.c
qtl/src/hmm_4way.h
qtl/src/hmm_ri8selfIRIP1.c
qtl/src/fitqtl_hk.h
qtl/src/scanone_hk.h
qtl/src/scantwo_em.c
qtl/src/hmm_bgmagic16.h
qtl/src/scanone_hk_binary.c
qtl/src/mqmmixture.h
qtl/src/scantwo_hk.c
qtl/src/scantwo_binary_hk.c
qtl/src/hmm_ri8self.c
qtl/src/fitqtl_imp.h
qtl/src/hmm_ri4sib.c
qtl/src/zeroin.c
qtl/src/mqmscan.cpp
qtl/src/scantwo_mr.h
qtl/src/lapackutil.c
qtl/src/hmm_ri4self.c
qtl/src/scantwo_imp.h
qtl/src/fitqtl_hk.c
qtl/src/ripple.h
qtl/src/scanone_hk.c
qtl/src/pickMarkerSubset.h
qtl/src/hmm_4way.c
qtl/src/zeroin.h
qtl/src/fill_geno_nodblXO.c
qtl/src/markerlrt.c
qtl/src/scantwo_hk.h
qtl/src/pickMarkerSubset.c
qtl/src/effectscan.h
qtl/src/discan.h
qtl/src/hmm_ri4self.h
qtl/src/scanone_em_covar.c
qtl/src/discan_covar.c
qtl/src/mqmdatatypes.h
qtl/src/summary_scantwo.c
qtl/src/findDupMarkers_notexact.c
qtl/src/countXO.h
qtl/src/scanone_np.h
qtl/src/scanone_imp.h
qtl/src/ril48_reorg.c
qtl/src/info.h
qtl/src/hmm_main.c
qtl/src/discan.c
qtl/src/simulate_ril.h
qtl/src/hmm_f2.h
qtl/src/forwsel.c
qtl/src/mqmaugment.cpp
qtl/src/stahl_mf.h
qtl/src/hmm_bc.h
qtl/NAMESPACE
qtl/data
qtl/data/bristleX.RData
qtl/data/fake.f2.RData
qtl/data/listeria.RData
qtl/data/map10.RData
qtl/data/hyper.RData
qtl/data/locations.RData
qtl/data/multitrait.RData
qtl/data/fake.4way.RData
qtl/data/fake.bc.RData
qtl/data/badorder.RData
qtl/data/bristle3.RData
qtl/data/mapthis.RData
qtl/R
qtl/R/read.cross.gary.R
qtl/R/refineqtl.R
qtl/R/scantwo.R
qtl/R/sim.geno.R
qtl/R/est.map.R
qtl/R/mqmaugment.R
qtl/R/plotperm.R
qtl/R/markerlrt.R
qtl/R/cim.R
qtl/R/inferFounderHap.R
qtl/R/map_construction.R
qtl/R/plot.scanone.R
qtl/R/scanone.R
qtl/R/scanonevar.varperm.R
qtl/R/stepwiseqtlX.R
qtl/R/read.cross.R
qtl/R/transformPheno.R
qtl/R/effectscan.R
qtl/R/addmarker.R
qtl/R/plot.R
qtl/R/fitstahl.R
qtl/R/ripple.R
qtl/R/plot.scantwo.R
qtl/R/scantwopermhk.R
qtl/R/plotModel.R
qtl/R/readMWril.R
qtl/R/vbscan.R
qtl/R/scanonevar.meanperm.R
qtl/R/add_threshold.R
qtl/R/write.cross.mq.R
qtl/R/errorlod.R
qtl/R/summary.scantwo.old.R
qtl/R/mqmcircleplot.R
qtl/R/read.cross.csvs.R
qtl/R/summary.cross.R
qtl/R/mqmsnow.R
qtl/R/pickMarkerSubset.R
qtl/R/calc.pairprob.R
qtl/R/mqmplots.R
qtl/R/argmax.geno.R
qtl/R/arithscan.R
qtl/R/addqtl.R
qtl/R/est.rf.R
qtl/R/summary.scanone.R
qtl/R/mqmscanall.R
qtl/R/write.cross.qtab.R
qtl/R/write.cross.R
qtl/R/scanqtl.R
qtl/R/effectplot.R
qtl/R/xchr.R
qtl/R/pull_stuff.R
qtl/R/read.cross.csv.R
qtl/R/mqmpermutation.R
qtl/R/viridis.R
qtl/R/tryallpositions.R
qtl/R/read.cross.karl.R
qtl/R/phyloqtl_util.R
qtl/R/summary.scantwo.R
qtl/R/replacemap.R
qtl/R/mqmscan.R
qtl/R/bcsft.R
qtl/R/droponemarker.R
qtl/R/phyloqtl_sim.R
qtl/R/mqmutil.R
qtl/R/discan.R
qtl/R/fitqtl.R
qtl/R/simulate.R
qtl/R/mqmprepare.R
qtl/R/read.cross.mm.R
qtl/R/calc.genoprob.R
qtl/R/add.cim.covar.R
qtl/R/util.R
qtl/R/read.cross.mq.R
qtl/R/stepwiseqtl.R
qtl/R/makeqtl.R
qtl/R/scanonevar.R
qtl/R/scanoneboot.R
qtl/R/countXO.R
qtl/R/sim_ril.R
qtl/R/mqmcofactors.R
qtl/R/interpPositions.R
qtl/R/read.cross.tidy.R
qtl/R/compareorder.R
qtl/R/read.cross.qtx.R
qtl/R/qtlcart_io.R
qtl/R/phyloqtl_scan.R
qtl/R/ril48_reorg.R
qtl/vignettes
qtl/vignettes/fancyheadings.sty
qtl/vignettes/recombinationcount.pdf
qtl/vignettes/bcsft.Rnw
qtl/vignettes/genotypeprobabilities.pdf
qtl/vignettes/why_we_need_a_new_program.pdf
qtl/vignettes/goldensectionsearch.pdf
qtl/vignettes/plos.bst
qtl/vignettes/vignette.bib
qtl/MD5
qtl/build
qtl/build/vignette.rds
qtl/DESCRIPTION
qtl/man
qtl/man/mqmplotheatmap.Rd
qtl/man/replacemap.scantwo.Rd
qtl/man/orderMarkers.Rd
qtl/man/add.threshold.Rd
qtl/man/scanonevar.Rd
qtl/man/mqmtestnormal.Rd
qtl/man/nmar.Rd
qtl/man/mqmplotpermutations.Rd
qtl/man/plot.scantwoperm.Rd
qtl/man/pull.geno.Rd
qtl/man/geno.crosstab.Rd
qtl/man/bristle3.Rd
qtl/man/compareorder.Rd
qtl/man/summary.scantwo.Rd
qtl/man/summary.scantwo.old.Rd
qtl/man/scanPhyloQTL.Rd
qtl/man/condense.scantwo.Rd
qtl/man/pull.pheno.Rd
qtl/man/est.map.Rd
qtl/man/getid.Rd
qtl/man/drop.nullmarkers.Rd
qtl/man/mqmplotdirectedqtl.Rd
qtl/man/scantwo.Rd
qtl/man/replaceqtl.Rd
qtl/man/tryallpositions.Rd
qtl/man/convert2sa.Rd
qtl/man/scanonevar.meanperm.Rd
qtl/man/addmarker.Rd
qtl/man/cleanGeno.Rd
qtl/man/summary.scanoneperm.Rd
qtl/man/simPhyloQTL.Rd
qtl/man/totmar.Rd
qtl/man/multitrait.Rd
qtl/man/nqtl.Rd
qtl/man/markerlrt.Rd
qtl/man/markernames.Rd
qtl/man/plotModel.Rd
qtl/man/mqmscan.Rd
qtl/man/nphe.Rd
qtl/man/makeqtl.Rd
qtl/man/mqmgetmodel.Rd
qtl/man/inferFounderHap.Rd
qtl/man/pull.markers.Rd
qtl/man/bristleX.Rd
qtl/man/summary.qtl.Rd
qtl/man/bayesint.Rd
qtl/man/plot.scantwo.Rd
qtl/man/subset.scantwo.Rd
qtl/man/summary.scanoneboot.Rd
qtl/man/nind.Rd
qtl/man/plot.errorlod.Rd
qtl/man/mqmplotclusteredheatmap.Rd
qtl/man/plot.qtl.Rd
qtl/man/max.scanPhyloQTL.Rd
qtl/man/movemarker.Rd
qtl/man/geno.table.Rd
qtl/man/interpPositions.Rd
qtl/man/find.markerpos.Rd
qtl/man/find.pseudomarker.Rd
qtl/man/c.cross.Rd
qtl/man/table2map.Rd
qtl/man/drop.markers.Rd
qtl/man/switch.order.Rd
qtl/man/convert2riself.Rd
qtl/man/comparecrosses.Rd
qtl/man/mqmautocofactors.Rd
qtl/man/nmissing.Rd
qtl/man/map2table.Rd
qtl/man/summary.map.Rd
qtl/man/cbind.scanoneperm.Rd
qtl/man/subset.scanone.Rd
qtl/man/convert.map.Rd
qtl/man/plot.pxg.Rd
qtl/man/strip.partials.Rd
qtl/man/summary.ripple.Rd
qtl/man/scanqtl.Rd
qtl/man/a.starting.point.Rd
qtl/man/clean.cross.Rd
qtl/man/stepwiseqtl.Rd
qtl/man/mapthis.Rd
qtl/man/ripple.Rd
qtl/man/shiftmap.Rd
qtl/man/addloctocross.Rd
qtl/man/hyper.Rd
qtl/man/scanonevar.varperm.Rd
qtl/man/plot.cross.Rd
qtl/man/mqmplotmultitrait.Rd
qtl/man/badorder.Rd
qtl/man/addcovarint.Rd
qtl/man/findmarkerindex.Rd
qtl/man/replacemap.scanone.Rd
qtl/man/plot.geno.Rd
qtl/man/addtoqtl.Rd
qtl/man/max.scantwo.Rd
qtl/man/xaxisloc.scanone.Rd
qtl/man/groupclusteredheatmap.Rd
qtl/man/plot.scanone.Rd
qtl/man/reduce2grid.Rd
qtl/man/transformPheno.Rd
qtl/man/refineqtl.Rd
qtl/man/countXO.Rd
qtl/man/pull.rf.Rd
qtl/man/pull.map.Rd
qtl/man/effectplot.Rd
qtl/man/summary.scanPhyloQTL.Rd
qtl/man/scanoneboot.Rd
qtl/man/checkAlleles.Rd
qtl/man/mqmfind.marker.Rd
qtl/man/subset.cross.Rd
qtl/man/findDupMarkers.Rd
qtl/man/sim.geno.Rd
qtl/man/formLinkageGroups.Rd
qtl/man/pickMarkerSubset.Rd
qtl/man/fake.f2.Rd
qtl/man/map10.Rd
qtl/man/replace.map.Rd
qtl/man/chrnames.Rd
qtl/man/fake.bc.Rd
qtl/man/readMWril.Rd
qtl/man/switchAlleles.Rd
qtl/man/plot.scanoneboot.Rd
qtl/man/listeria.Rd
qtl/man/summary.cross.Rd
qtl/man/comparegeno.Rd
qtl/man/pull.argmaxgeno.Rd
qtl/man/dropfromqtl.Rd
qtl/man/calc.errorlod.Rd
qtl/man/simulateMissingData.Rd
qtl/man/scantwopermhk.Rd
qtl/man/summary.scantwoperm.Rd
qtl/man/est.rf.Rd
qtl/man/mqmaugment.Rd
qtl/man/qtlversion.Rd
qtl/man/droponemarker.Rd
qtl/man/summary.scanone.Rd
qtl/man/mqmpermutation.Rd
qtl/man/fitstahl.Rd
qtl/man/c.scantwo.Rd
qtl/man/mqmplotcircle.Rd
qtl/man/find.flanking.Rd
qtl/man/flip.order.Rd
qtl/man/plot.pheno.Rd
qtl/man/geno.image.Rd
qtl/man/lodint.Rd
qtl/man/c.scanoneperm.Rd
qtl/man/top.errorlod.Rd
qtl/man/drop.dupmarkers.Rd
qtl/man/subset.map.Rd
qtl/man/formMarkerCovar.Rd
qtl/man/plot.rf.Rd
qtl/man/add.cim.covar.Rd
qtl/man/fill.geno.Rd
qtl/man/plot.scanPhyloQTL.Rd
qtl/man/max.scanone.Rd
qtl/man/chrlen.Rd
qtl/man/rescalemap.Rd
qtl/man/summary.fitqtl.Rd
qtl/man/c.scantwoperm.Rd
qtl/man/write.cross.Rd
qtl/man/inferredpartitions.Rd
qtl/man/subset.scanoneperm.Rd
qtl/man/addpair.Rd
qtl/man/mqmplotcistrans.Rd
qtl/man/convert.scantwo.Rd
qtl/man/reorderqtl.Rd
qtl/man/nchr.Rd
qtl/man/nqrank.Rd
qtl/man/pull.draws.Rd
qtl/man/pull.genoprob.Rd
qtl/man/clean.scantwo.Rd
qtl/man/arithscan.Rd
qtl/man/sim.map.Rd
qtl/man/mqmsetcofactors.Rd
qtl/man/MQM.Rd
qtl/man/phenames.Rd
qtl/man/nullmarkers.Rd
qtl/man/fitqtl.Rd
qtl/man/plot.info.Rd
qtl/man/plot.scanoneperm.Rd
qtl/man/cbind.scantwoperm.Rd
qtl/man/ntyped.Rd
qtl/man/plot.missing.Rd
qtl/man/addint.Rd
qtl/man/find.pheno.Rd
qtl/man/calc.penalties.Rd
qtl/man/read.cross.Rd
qtl/man/mqmextractmarkers.Rd
qtl/man/plot.map.Rd
qtl/man/effectscan.Rd
qtl/man/fake.4way.Rd
qtl/man/typingGap.Rd
qtl/man/locateXO.Rd
qtl/man/mqmscanfdr.Rd
qtl/man/plot.rfmatrix.Rd
qtl/man/mqmscanall.Rd
qtl/man/arithscanperm.Rd
qtl/man/locations.Rd
qtl/man/simFounderSnps.Rd
qtl/man/addqtl.Rd
qtl/man/convert2risib.Rd
qtl/man/convert.scanone.Rd
qtl/man/mqmprocesspermutation.Rd
qtl/man/c.scanone.Rd
qtl/man/calc.genoprob.Rd
qtl/man/sim.cross.Rd
qtl/man/plotLodProfile.Rd
qtl/man/jittermap.Rd
qtl/man/cim.Rd
qtl/man/allchrsplits.Rd
qtl/man/mqmplotsingletrait.Rd
qtl/man/subset.scantwoperm.Rd
qtl/man/find.marker.Rd
qtl/man/argmax.geno.Rd
qtl/man/qtl-internal.Rd
qtl/man/mqmplotcofactors.Rd
qtl/man/scanone.Rd