Files in qtl
Tools for Analyzing QTL Experiments

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/R_init.h
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/R_init.c
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 June 20, 2017, 9:05 a.m.