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