qtl: Tools for Analyzing QTL Experiments
Version 1.40-8

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

AuthorKarl 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 publication2016-11-05 08:59:40
MaintainerKarl W Broman <kbroman@biostat.wisc.edu>
LicenseGPL-3
Version1.40-8
URL http://rqtl.org
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("qtl")

Popular man pages

c.cross: Combine data for QTL experiments
cim: Composite interval mapping
find.marker: Find marker closest to a specified position
fitqtl: Fit a multiple-QTL model
lodint: LOD support interval
plot.pxg: Plot phenotypes versus marker genotypes
read.cross: Read data for a QTL experiment
See all...

All man pages Function index File listing

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

Functions

Files

inst
inst/BUGS.txt
inst/CITATION
inst/TODO.txt
inst/STATUS.txt
inst/LICENSE.txt
inst/MQM-TODO.txt
inst/README.md
inst/INSTALL_ME.txt
inst/doc
inst/doc/geneticmaps.pdf
inst/doc/Sources
inst/doc/Sources/new_multiqtl.Rnw
inst/doc/Sources/rqtltour.tex
inst/doc/Sources/rqtltour2.tex
inst/doc/Sources/new_summary_scantwo.Rnw
inst/doc/Sources/geneticmaps.Rnw
inst/doc/Sources/new_summary_scanone.Rnw
inst/doc/Sources/MQM
inst/doc/Sources/MQM/sweaveit.sh
inst/doc/Sources/MQM/MQM-tour.Rnw
inst/doc/Sources/MQM/mqm
inst/doc/Sources/MQM/mqm/description.txt
inst/doc/Sources/MQM/mqm/standard_references.txt
inst/doc/Sources/MQM/mqm/standard_example.txt
inst/doc/Sources/MQM/mqm/standard_seealso.txt
inst/doc/Sources/MQM/mqm/limitations.txt
inst/doc/Sources/MQM/mqm/advantages_latex.txt
inst/doc/Sources/MQM/mqm/advantages_Rd.txt
inst/doc/Sources/MQM/mqm/significance_references.txt
inst/doc/Sources/MQM/mqm/parallelisation_references.txt
inst/doc/Sources/MQM/SweaveIt.R
inst/doc/Sources/MQM/sweaveit.bat
inst/doc/bcsft.pdf
inst/doc/new_multiqtl.R
inst/doc/rqtltour2.pdf
inst/doc/rqtltour2.R
inst/doc/bcsft.Rnw
inst/doc/new_summary_scantwo.pdf
inst/doc/geneticmaps.R
inst/doc/new_multiqtl.pdf
inst/doc/bcsft.R
inst/doc/new_summary_scanone.R
inst/doc/rqtltour.R
inst/doc/rqtltour.pdf
inst/doc/new_summary_scantwo.R
inst/doc/new_summary_scanone.pdf
inst/contrib
inst/contrib/biolib
inst/contrib/biolib/CMakeLists.txt
inst/contrib/biolib/README
inst/contrib/scripts
inst/contrib/scripts/check_rqtl.sh
inst/contrib/scripts/cleanup.sh
inst/contrib/scripts/repl_inputs.rb
inst/contrib/scripts/run_all_tests.sh
inst/contrib/scripts/update_header.rb
inst/contrib/scripts/install_rqtl.sh
inst/contrib/bin
inst/contrib/bin/mqmdebugout.cpp
inst/contrib/bin/CMakeLists.txt
inst/contrib/bin/wincompile.bat
inst/contrib/bin/scripts
inst/contrib/bin/scripts/cleanup.sh
inst/contrib/bin/scripts/profiler.sh
inst/contrib/bin/scripts/r.sh
inst/contrib/bin/scripts/regression_tests.sh
inst/contrib/bin/scripts/create-diff.sh
inst/contrib/bin/scripts/regression_tests_windows.bat
inst/contrib/bin/mqmmain.cpp
inst/contrib/bin/README
inst/contrib/bin/FindRLibs.cmake
inst/contrib/bin/regressiontests.bat
inst/contrib/bin/test
inst/contrib/bin/test/chridhyper.txt
inst/contrib/bin/test/filledgenohyper.txt
inst/contrib/bin/test/t12
inst/contrib/bin/test/t12/cofactors.txt
inst/contrib/bin/test/settingshyper.txt
inst/contrib/bin/test/phenohyper.txt
inst/contrib/bin/test/pheno.dat
inst/contrib/bin/test/genohyper.txt
inst/contrib/bin/test/t11
inst/contrib/bin/test/t11/cofactors.txt
inst/contrib/bin/test/regression
inst/contrib/bin/test/regression/t25out.txt
inst/contrib/bin/test/regression/t24out.txt
inst/contrib/bin/test/regression/t33out.txt
inst/contrib/bin/test/regression/t11out-test0.txt
inst/contrib/bin/test/regression/t32out.txt
inst/contrib/bin/test/regression/debugout_pbeta.txt
inst/contrib/bin/test/regression/debugout_dnorm.txt
inst/contrib/bin/test/regression/t34out.txt
inst/contrib/bin/test/regression/t12out.txt
inst/contrib/bin/test/regression/t31out.txt
inst/contrib/bin/test/regression/t21out.txt
inst/contrib/bin/test/regression/t13out.txt
inst/contrib/bin/test/regression/t23out.txt
inst/contrib/bin/test/regression/t22out.txt
inst/contrib/bin/test/regression/t11out.txt
inst/contrib/bin/test/cofactors.txt
inst/contrib/bin/test/std
inst/contrib/bin/test/std/settings3.txt
inst/contrib/bin/test/std/phenotypes2.txt
inst/contrib/bin/test/std/settings2.txt
inst/contrib/bin/test/std/genotypes3.txt
inst/contrib/bin/test/std/genotypes2.txt
inst/contrib/bin/test/std/genotypes1.txt
inst/contrib/bin/test/std/phenotypes3.txt
inst/contrib/bin/test/std/genotypes2m.txt
inst/contrib/bin/test/std/markers1.txt
inst/contrib/bin/test/std/settings1.txt
inst/contrib/bin/test/std/markers2.txt
inst/contrib/bin/test/std/genotypes3m.txt
inst/contrib/bin/test/std/markers3.txt
inst/contrib/bin/test/std/phenotypes1.txt
inst/contrib/bin/test/t33
inst/contrib/bin/test/t33/cofactors.txt
inst/contrib/bin/test/settings.dat
inst/contrib/bin/test/geno.dat
inst/contrib/bin/test/chrid.dat
inst/contrib/bin/test/t23
inst/contrib/bin/test/t23/cofactors.txt
inst/contrib/bin/test/markerpos.txt
inst/contrib/bin/test/t22
inst/contrib/bin/test/t22/cofactors.txt
inst/contrib/bin/test/markerposhyper.txt
inst/contrib/bin/rtest
inst/contrib/bin/rtest/test_mqm_hyper_prob.R
inst/contrib/bin/rtest/regression
inst/contrib/bin/rtest/regression/scanone_mr.rtest
inst/contrib/bin/rtest/regression/mqm_listeria1.rtest
inst/contrib/bin/rtest/test_mqm_listeria1.R
inst/contrib/bin/rtest/test_augmentation.R
inst/contrib/bin/rtest/test_scanone_mr.R
inst/sampledata
inst/sampledata/listeria_qc_cro.txt
inst/sampledata/listeria_qc_map.txt
inst/sampledata/listeria.csv
inst/sampledata/gen.txt
inst/sampledata/listeria_gen_rot.csv
inst/sampledata/listeria_phe_rot.csv
inst/sampledata/listeria_gen.csv
inst/sampledata/listeria_rot.csv
inst/sampledata/listeria.qtx
inst/sampledata/phe.txt
inst/sampledata/listeria_phe.csv
inst/sampledata/listeria_maps.txt
inst/sampledata/map.txt
inst/sampledata/README.txt
inst/sampledata/listeria_raw.txt
inst/sampledata/listeria_map.txt
tests
tests/listeria.csv
tests/gen.txt
tests/listeria.map
tests/test_scanonevar.R
tests/test_io.R
tests/testaugmentation.R
tests/test_tidyIO.Rout.save
tests/test_io.Rout.save
tests/phe.txt
tests/listeria2.map
tests/test_qtl.R
tests/test_mapqtl_io.R
tests/map.txt
tests/test_mapqtl_io.Rout.save
tests/testthat.R
tests/listeria2.csv
tests/testthat
tests/testthat/test-scantwoperm.R
tests/testthat/test-fliporder.R
tests/testthat/test-stepwiseqtl.R
tests/listeria.raw
tests/test_tidyIO.R
tests/test_scanonevar.Rout.save
src
src/hmm_main.h
src/mqmprob.cpp
src/mqmmixture.cpp
src/hmm_bcsft.h
src/fitqtl_imp_binary.h
src/fitqtl_imp_binary.c
src/Makevars
src/util.c
src/scanone_em.h
src/markerlrt.h
src/scantwo_binary_em.h
src/mqmdatatypes.cpp
src/mqmmapqtl.cpp
src/scantwo_imp.c
src/fitqtl_imp.c
src/hmm_ri4sib.h
src/simulate.c
src/hmm_util.c
src/hmm_bci.c
src/stahl_mf.c
src/inferFounderHap.h
src/scantwo_em.h
src/hmm_bgmagic16.c
src/hmm_ri8self.h
src/mqmeliminate.h
src/effectscan.c
src/scanone_mr.h
src/mqmeliminate.cpp
src/fitqtl_hk_binary.c
src/hmm_f2i.c
src/scanone_imp.c
src/ril48_reorg.h
src/hmm_ri8sib.c
src/vbscan.h
src/fill_geno_nodblXO.h
src/mqmregression.cpp
src/scanone_hk_binary.h
src/hmm_ri8sib.h
src/scantwopermhk.c
src/scanone_em_covar.h
src/hmm_f2i.h
src/discan_covar.h
src/hmm_bci.h
src/ripple.c
src/forwsel.h
src/simulate_ril.c
src/scanone_ehk.c
src/hmm_ri8selfIRIP1.h
src/mqmscan.h
src/mqmregression.h
src/scantwo_mr.c
src/standalone.h
src/test_bcsft.c
src/countXO.c
src/mqm.h
src/hmm_bcsft.c
src/mqmmapqtl.h
src/hmm_bc.c
src/hmm_util.h
src/scantwo_binary_hk.h
src/scanone_np.c
src/info.c
src/scanone_ehk.h
src/lapackutil.h
src/scanone_em.c
src/vbscan.c
src/simulate.h
src/scantwo_binary_em.c
src/util.h
src/summary_scantwo.h
src/scanone_mr.c
src/findDupMarkers_notexact.h
src/mqmprob.h
src/hmm_f2.c
src/mqmaugment.h
src/scantwopermhk.h
src/fitqtl_hk_binary.h
src/inferFounderHap.c
src/hmm_4way.h
src/hmm_ri8selfIRIP1.c
src/fitqtl_hk.h
src/scanone_hk.h
src/scantwo_em.c
src/hmm_bgmagic16.h
src/scanone_hk_binary.c
src/mqmmixture.h
src/scantwo_hk.c
src/scantwo_binary_hk.c
src/hmm_ri8self.c
src/fitqtl_imp.h
src/hmm_ri4sib.c
src/zeroin.c
src/mqmscan.cpp
src/scantwo_mr.h
src/lapackutil.c
src/hmm_ri4self.c
src/scantwo_imp.h
src/fitqtl_hk.c
src/ripple.h
src/scanone_hk.c
src/pickMarkerSubset.h
src/hmm_4way.c
src/zeroin.h
src/fill_geno_nodblXO.c
src/markerlrt.c
src/scantwo_hk.h
src/pickMarkerSubset.c
src/effectscan.h
src/discan.h
src/hmm_ri4self.h
src/scanone_em_covar.c
src/discan_covar.c
src/mqmdatatypes.h
src/summary_scantwo.c
src/findDupMarkers_notexact.c
src/countXO.h
src/scanone_np.h
src/scanone_imp.h
src/ril48_reorg.c
src/info.h
src/hmm_main.c
src/discan.c
src/simulate_ril.h
src/hmm_f2.h
src/forwsel.c
src/mqmaugment.cpp
src/stahl_mf.h
src/hmm_bc.h
NAMESPACE
data
data/bristleX.RData
data/fake.f2.RData
data/listeria.RData
data/map10.RData
data/hyper.RData
data/locations.RData
data/multitrait.RData
data/fake.4way.RData
data/fake.bc.RData
data/badorder.RData
data/bristle3.RData
data/mapthis.RData
R
R/read.cross.gary.R
R/refineqtl.R
R/scantwo.R
R/sim.geno.R
R/est.map.R
R/mqmaugment.R
R/plotperm.R
R/markerlrt.R
R/cim.R
R/inferFounderHap.R
R/map_construction.R
R/plot.scanone.R
R/scanone.R
R/scanonevar.varperm.R
R/stepwiseqtlX.R
R/read.cross.R
R/transformPheno.R
R/effectscan.R
R/addmarker.R
R/plot.R
R/fitstahl.R
R/ripple.R
R/plot.scantwo.R
R/scantwopermhk.R
R/plotModel.R
R/readMWril.R
R/vbscan.R
R/scanonevar.meanperm.R
R/add_threshold.R
R/write.cross.mq.R
R/errorlod.R
R/summary.scantwo.old.R
R/mqmcircleplot.R
R/read.cross.csvs.R
R/summary.cross.R
R/mqmsnow.R
R/pickMarkerSubset.R
R/calc.pairprob.R
R/mqmplots.R
R/argmax.geno.R
R/arithscan.R
R/addqtl.R
R/est.rf.R
R/summary.scanone.R
R/mqmscanall.R
R/write.cross.qtab.R
R/write.cross.R
R/scanqtl.R
R/effectplot.R
R/xchr.R
R/pull_stuff.R
R/read.cross.csv.R
R/mqmpermutation.R
R/viridis.R
R/tryallpositions.R
R/read.cross.karl.R
R/phyloqtl_util.R
R/summary.scantwo.R
R/replacemap.R
R/mqmscan.R
R/bcsft.R
R/droponemarker.R
R/phyloqtl_sim.R
R/mqmutil.R
R/discan.R
R/fitqtl.R
R/simulate.R
R/mqmprepare.R
R/read.cross.mm.R
R/calc.genoprob.R
R/add.cim.covar.R
R/util.R
R/read.cross.mq.R
R/stepwiseqtl.R
R/makeqtl.R
R/scanonevar.R
R/scanoneboot.R
R/countXO.R
R/sim_ril.R
R/mqmcofactors.R
R/interpPositions.R
R/read.cross.tidy.R
R/compareorder.R
R/read.cross.qtx.R
R/qtlcart_io.R
R/phyloqtl_scan.R
R/ril48_reorg.R
vignettes
vignettes/fancyheadings.sty
vignettes/recombinationcount.pdf
vignettes/bcsft.Rnw
vignettes/genotypeprobabilities.pdf
vignettes/why_we_need_a_new_program.pdf
vignettes/goldensectionsearch.pdf
vignettes/plos.bst
vignettes/vignette.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/mqmplotheatmap.Rd
man/replacemap.scantwo.Rd
man/orderMarkers.Rd
man/add.threshold.Rd
man/scanonevar.Rd
man/mqmtestnormal.Rd
man/nmar.Rd
man/mqmplotpermutations.Rd
man/plot.scantwoperm.Rd
man/pull.geno.Rd
man/geno.crosstab.Rd
man/bristle3.Rd
man/compareorder.Rd
man/summary.scantwo.Rd
man/summary.scantwo.old.Rd
man/scanPhyloQTL.Rd
man/condense.scantwo.Rd
man/pull.pheno.Rd
man/est.map.Rd
man/getid.Rd
man/drop.nullmarkers.Rd
man/mqmplotdirectedqtl.Rd
man/scantwo.Rd
man/replaceqtl.Rd
man/tryallpositions.Rd
man/convert2sa.Rd
man/scanonevar.meanperm.Rd
man/addmarker.Rd
man/cleanGeno.Rd
man/summary.scanoneperm.Rd
man/simPhyloQTL.Rd
man/totmar.Rd
man/multitrait.Rd
man/nqtl.Rd
man/markerlrt.Rd
man/markernames.Rd
man/plotModel.Rd
man/mqmscan.Rd
man/nphe.Rd
man/makeqtl.Rd
man/mqmgetmodel.Rd
man/inferFounderHap.Rd
man/pull.markers.Rd
man/bristleX.Rd
man/summary.qtl.Rd
man/bayesint.Rd
man/plot.scantwo.Rd
man/subset.scantwo.Rd
man/summary.scanoneboot.Rd
man/nind.Rd
man/plot.errorlod.Rd
man/mqmplotclusteredheatmap.Rd
man/plot.qtl.Rd
man/max.scanPhyloQTL.Rd
man/movemarker.Rd
man/geno.table.Rd
man/interpPositions.Rd
man/find.markerpos.Rd
man/find.pseudomarker.Rd
man/c.cross.Rd
man/table2map.Rd
man/drop.markers.Rd
man/switch.order.Rd
man/convert2riself.Rd
man/comparecrosses.Rd
man/mqmautocofactors.Rd
man/nmissing.Rd
man/map2table.Rd
man/summary.map.Rd
man/cbind.scanoneperm.Rd
man/subset.scanone.Rd
man/convert.map.Rd
man/plot.pxg.Rd
man/strip.partials.Rd
man/summary.ripple.Rd
man/scanqtl.Rd
man/a.starting.point.Rd
man/clean.cross.Rd
man/stepwiseqtl.Rd
man/mapthis.Rd
man/ripple.Rd
man/shiftmap.Rd
man/addloctocross.Rd
man/hyper.Rd
man/scanonevar.varperm.Rd
man/plot.cross.Rd
man/mqmplotmultitrait.Rd
man/badorder.Rd
man/addcovarint.Rd
man/findmarkerindex.Rd
man/replacemap.scanone.Rd
man/plot.geno.Rd
man/addtoqtl.Rd
man/max.scantwo.Rd
man/xaxisloc.scanone.Rd
man/groupclusteredheatmap.Rd
man/plot.scanone.Rd
man/reduce2grid.Rd
man/transformPheno.Rd
man/refineqtl.Rd
man/countXO.Rd
man/pull.rf.Rd
man/pull.map.Rd
man/effectplot.Rd
man/summary.scanPhyloQTL.Rd
man/scanoneboot.Rd
man/checkAlleles.Rd
man/mqmfind.marker.Rd
man/subset.cross.Rd
man/findDupMarkers.Rd
man/sim.geno.Rd
man/formLinkageGroups.Rd
man/pickMarkerSubset.Rd
man/fake.f2.Rd
man/map10.Rd
man/replace.map.Rd
man/chrnames.Rd
man/fake.bc.Rd
man/readMWril.Rd
man/switchAlleles.Rd
man/plot.scanoneboot.Rd
man/listeria.Rd
man/summary.cross.Rd
man/comparegeno.Rd
man/pull.argmaxgeno.Rd
man/dropfromqtl.Rd
man/calc.errorlod.Rd
man/simulateMissingData.Rd
man/scantwopermhk.Rd
man/summary.scantwoperm.Rd
man/est.rf.Rd
man/mqmaugment.Rd
man/qtlversion.Rd
man/droponemarker.Rd
man/summary.scanone.Rd
man/mqmpermutation.Rd
man/fitstahl.Rd
man/c.scantwo.Rd
man/mqmplotcircle.Rd
man/find.flanking.Rd
man/flip.order.Rd
man/plot.pheno.Rd
man/geno.image.Rd
man/lodint.Rd
man/c.scanoneperm.Rd
man/top.errorlod.Rd
man/drop.dupmarkers.Rd
man/subset.map.Rd
man/formMarkerCovar.Rd
man/plot.rf.Rd
man/add.cim.covar.Rd
man/fill.geno.Rd
man/plot.scanPhyloQTL.Rd
man/max.scanone.Rd
man/chrlen.Rd
man/rescalemap.Rd
man/summary.fitqtl.Rd
man/c.scantwoperm.Rd
man/write.cross.Rd
man/inferredpartitions.Rd
man/subset.scanoneperm.Rd
man/addpair.Rd
man/mqmplotcistrans.Rd
man/convert.scantwo.Rd
man/reorderqtl.Rd
man/nchr.Rd
man/nqrank.Rd
man/pull.draws.Rd
man/pull.genoprob.Rd
man/clean.scantwo.Rd
man/arithscan.Rd
man/sim.map.Rd
man/mqmsetcofactors.Rd
man/MQM.Rd
man/phenames.Rd
man/nullmarkers.Rd
man/fitqtl.Rd
man/plot.info.Rd
man/plot.scanoneperm.Rd
man/cbind.scantwoperm.Rd
man/ntyped.Rd
man/plot.missing.Rd
man/addint.Rd
man/find.pheno.Rd
man/calc.penalties.Rd
man/read.cross.Rd
man/mqmextractmarkers.Rd
man/plot.map.Rd
man/effectscan.Rd
man/fake.4way.Rd
man/typingGap.Rd
man/locateXO.Rd
man/mqmscanfdr.Rd
man/plot.rfmatrix.Rd
man/mqmscanall.Rd
man/arithscanperm.Rd
man/locations.Rd
man/simFounderSnps.Rd
man/addqtl.Rd
man/convert2risib.Rd
man/convert.scanone.Rd
man/mqmprocesspermutation.Rd
man/c.scanone.Rd
man/calc.genoprob.Rd
man/sim.cross.Rd
man/plotLodProfile.Rd
man/jittermap.Rd
man/cim.Rd
man/allchrsplits.Rd
man/mqmplotsingletrait.Rd
man/subset.scantwoperm.Rd
man/find.marker.Rd
man/argmax.geno.Rd
man/qtl-internal.Rd
man/mqmplotcofactors.Rd
man/scanone.Rd
qtl documentation built on May 19, 2017, 8:49 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.