qtl: Tools for Analyzing QTL Experiments

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
http://rqtl.org

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

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