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qtl

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Tools for Analyzing QTL Experiments

View on CRAN: Click here

Download and install qtl package within the R console
Install from CRAN:

 install.packages("qtl")

Install from Github:

 library("remotes")

                        install_github("cran/qtl")

Install by package version:

 library("remotes")

                        install_version("qtl", "1.74")

Attach the package and use:

 library("qtl")

Maintained by
Karl W Broman
[Scholar Profile | Author Map]

All associated links for this package

First Published: 2001-10-30

Latest Update: 2024-08-22

Description:

Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) .

How to cite:

Karl W Broman (2001). qtl: Tools for Analyzing QTL Experiments. R package version 1.74, https://cran.r-project.org/web/packages/qtl. Accessed 26 Aug. 2026.

Previous versions and publish date:

(2026-07-09 06:45), 0.85-4 (2001-10-30 12:12), 0.92-3 (2002-02-12 20:57), 0.96-5 (2002-09-30 23:04), 0.97-21 (2003-06-21 00:21), 0.97-22 (2004-01-02 16:22), 0.98-57 (2004-09-12 10:03), 0.99-22 (2005-04-26 11:08), 0.99-24 (2005-04-27 10:32), 1.00-15 (2005-09-03 21:44), 1.00-16 (2005-09-04 14:25), 1.00-17 (2005-09-07 17:27), 1.01-9 (2005-10-25 22:28), 1.02-26 (2006-06-08 12:52), 1.03-14 (2006-07-21 10:26), 1.04-52 (2006-10-28 12:42), 1.04-53 (2006-10-29 10:40), 1.05-2 (2006-11-09 11:13), 1.06-43 (2007-08-09 15:01), 1.07-11 (2007-09-21 17:22), 1.07-12 (2007-10-09 22:12), 1.08-55 (2008-04-03 18:28), 1.08-56 (2008-04-09 09:14), 1.09-43 (2008-07-20 11:09), 1.10-27 (2009-01-11 22:26), 1.11-12 (2009-03-29 16:55), 1.12-26 (2009-07-01 14:04), 1.13-7 (2009-09-10 22:15), 1.14-2 (2009-10-01 21:55), 1.15-15 (2010-05-02 19:26), 1.16-4 (2010-05-16 18:20), 1.16-6 (2010-05-25 17:58), 1.17-39 (2010-07-29 11:14), 1.18-7 (2010-08-18 20:21), 1.19-20 (2010-11-30 09:05), 1.20-15 (2011-02-23 10:33), 1.21-2 (2011-03-21 16:34), 1.22-21 (2011-11-29 07:57), 1.23-16 (2012-03-06 20:04), 1.24-9 (2012-05-25 19:13), 1.25-15 (2012-08-14 08:57), 1.26-13 (2012-11-27 15:03), 1.26-14 (2012-11-27 21:25), 1.27-10 (2013-04-11 16:56), 1.28-19 (2013-09-23 23:09), 1.29-2 (2013-12-09 17:08), 1.30-4 (2014-02-11 00:55), 1.31-9 (2014-03-20 07:39), 1.32-10 (2014-05-29 18:40), 1.33-7 (2014-08-12 20:20), 1.34-16 (2014-10-29 19:20), 1.34-17 (2014-10-30 21:22), 1.35-1 (2014-12-13 00:20), 1.35-3 (2014-12-16 04:26), 1.36-6 (2015-03-06 00:47), 1.37-11 (2015-08-25 19:21), 1.38-4 (2015-12-03 16:24), 1.39-5 (2016-03-04 17:34), 1.40-8 (2016-11-05 08:59), 1.41-6 (2017-06-12 08:01), 1.42-7 (2018-02-18 16:31), 1.42-8 (2018-02-19 20:40), 1.44-9 (2019-01-22 18:30), 1.45-11 (2020-02-02 17:40), 1.46-2 (2020-03-12 00:10), 1.47-9 (2021-01-07 22:30), 1.48-1 (2021-03-27 09:40), 1.50 (2021-10-06 18:00), 1.52 (2022-07-09 16:50), 1.54 (2022-12-02 01:20), 1.58 (2023-01-07 19:50), 1.60 (2023-04-18 22:40), 1.62 (2023-11-17 22:00), 1.66 (2023-11-27 21:40), 1.70 (2024-08-22 04:20), 1.72 (2025-11-19 16:50)

Other packages that cited qtl R package

View qtl citation profile

Other R packages that qtl depends, imports, suggests or enhances

View qtl dependency map

Complete documentation for qtl

View documentation PDF

Functions, R codes and Examples using the qtl R package

Some associated functions: MQM . a.starting.point . add.cim.covar . add.threshold . addcovarint . addint . addloctocross . addmarker . addpair . addqtl . addtoqtl . allchrsplits . argmax.geno . arithscan . arithscanperm . badorder . bayesint . bristle3 . bristleX . c.cross . c.scanone . c.scanoneperm . c.scantwo . c.scantwoperm . calc.errorlod . calc.genoprob . calc.penalties . cbind.scanoneperm . cbind.scantwoperm . checkAlleles . chrlen . chrnames . cim . clean.cross . clean.scantwo . cleanGeno . comparecrosses . comparegeno . compareorder . condense.scantwo . convert.map . convert.scanone . convert.scantwo . convert2riself . convert2risib . convert2sa . countXO . drop.dupmarkers . drop.markers . drop.nullmarkers . dropfromqtl . droponemarker . effectplot . effectscan . est.map . est.rf . fake.4way . fake.bc . fake.f2 . fill.geno . find.flanking . find.marker . find.markerpos . find.pheno . find.pseudomarker . findDupMarkers . find_large_intervals . findmarkerindex . fitqtl . fitstahl . flip.order . formLinkageGroups . formMarkerCovar . geno.crosstab . geno.image . geno.table . getid . groupclusteredheatmap . hyper . inferFounderHap . inferredpartitions . interpPositions . jittermap . listeria . locateXO . locations . lodint . makeqtl . map10 . map2table . mapthis . markerlrt . markernames . max.scanPhyloQTL . max.scanone . max.scantwo . movemarker . mqmaugment . mqmautocofactors . mqmextractmarkers . mqmfind.marker . mqmgetmodel . mqmpermutation . mqmplotcircle . mqmplotcistrans . mqmplotclusteredheatmap . mqmplotcofactors . mqmplotdirectedqtl . mqmplotheatmap . mqmplotmultitrait . mqmplotpermutations . mqmplotsingletrait . mqmprocesspermutation . mqmscan . mqmscanall . mqmscanfdr . mqmsetcofactors . mqmtestnormal . multitrait . nchr . nind . nmar . nmissing . nphe . nqrank . nqtl . ntyped . nullmarkers . orderMarkers . phenames . pickMarkerSubset . plot.comparegeno . plot.cross . plot.errorlod . plot.geno . plot.info . plot.map . plot.missing . plot.pheno . plot.pxg . plot.qtl . plot.rf . plot.rfmatrix . plot.scanPhyloQTL . plot.scanone . plot.scanoneboot . plot.scanoneperm . plot.scantwo . plot.scantwoperm . plotLodProfile . plotModel . pull.argmaxgeno . pull.draws . pull.geno . pull.genoprob . pull.map . pull.markers . pull.pheno . pull.rf . qtl-internal . qtlversion . read.cross . readMWril . reduce2grid . refineqtl . reorderqtl . replace.map . replacemap.scanone . replacemap.scantwo . replaceqtl . rescalemap . ripple . scanPhyloQTL . scanone . scanoneboot . scanonevar.meanperm . scanonevar . scanonevar.varperm . scanqtl . scantwo . scantwopermhk . shiftmap . sim.cross . sim.geno . sim.map . simFounderSnps . simPhyloQTL . simulateMissingData . stepwiseqtl . strip.partials . subset.cross . subset.map . subset.scanone . subset.scanoneperm . subset.scantwo . subset.scantwoperm . summary.comparegeno . summary.cross . summary.fitqtl . summary.map . summary.qtl . summary.ripple . summary.scanPhyloQTL . summary.scanone . summary.scanoneboot . summary.scanoneperm . summary.scantwo . summary.scantwo.old . summary.scantwoperm . switch.order . switchAlleles . table2map . top.errorlod . totmar . transformPheno . tryallpositions . typingGap . write.cross . xaxisloc.scanone .
Some associated R codes: add.cim.covar.R . add_threshold.R . addmarker.R . addqtl.R . argmax.geno.R . arithscan.R . bcsft.R . calc.genoprob.R . calc.pairprob.R . cim.R . comparegeno.R . compareorder.R . countXO.R . discan.R . droponemarker.R . effectplot.R . effectscan.R . errorlod.R . est.map.R . est.rf.R . find_large_intervals.R . fitqtl.R . fitstahl.R . inferFounderHap.R . interpPositions.R . makeqtl.R . map_construction.R . markerlrt.R . mqmaugment.R . mqmcircleplot.R . mqmcofactors.R . mqmpermutation.R . mqmplots.R . mqmprepare.R . mqmscan.R . mqmscanall.R . mqmsnow.R . mqmutil.R . phyloqtl_scan.R . phyloqtl_sim.R . phyloqtl_util.R . pickMarkerSubset.R . plot.R . plot.scanone.R . plot.scantwo.R . plotModel.R . plotperm.R . pull_stuff.R . qtlcart_io.R . read.cross.R . read.cross.csv.R . read.cross.csvs.R . read.cross.gary.R . read.cross.karl.R . read.cross.mm.R . read.cross.mq.R . read.cross.qtx.R . read.cross.tidy.R . readMWril.R . refineqtl.R . replacemap.R . ril48_reorg.R . ripple.R . scanone.R . scanoneboot.R . scanonevar.R . scanonevar.meanperm.R . scanonevar.varperm.R . scanqtl.R . scantwo.R . scantwopermhk.R . sim.geno.R . sim_ril.R . simulate.R . stepwiseqtl.R . stepwiseqtlX.R . summary.cross.R . summary.scanone.R . summary.scantwo.R . summary.scantwo.old.R . transformPheno.R . tryallpositions.R . util.R . vbscan.R . viridis.R . write.cross.R . write.cross.mq.R . write.cross.qtab.R . xchr.R . Full qtl package functions and examples

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