[ol8_developer_EPEL] R-qtl-1.47.9-1.el8.aarch64

R-qtl is an extensible, interactive environment for mapping
quantitative trait loci (QTLs) in experimental crosses. Our goal is to
make complex QTL mapping methods widely accessible and allow users to
focus on modeling rather than computing.

A key component of computational methods for QTL mapping is the hidden
Markov model (HMM) technology for dealing with missing genotype
data. We have implemented the main HMM algorithms, with allowance for
the presence of genotyping errors, for backcrosses, intercrosses, and
phase-known four-way crosses.

The current version of R-qtl includes facilities for estimating
genetic maps, identifying genotyping errors, and performing single-QTL
genome scans and two-QTL, two-dimensional genome scans, by interval
mapping (with the EM algorithm), Haley-Knott regression, and multiple
imputation. All of this may be done in the presence of covariates
(such as sex, age or treatment). One may also fit higher-order QTL
models by multiple imputation and Haley-Knott regression.

Filelist (Show Changelog) (Show related packages)

• /

  • usr

    • lib

      • .build-id

        • 05

          • 19600e4167c80982c8570460dbdfd2a88c809f

    • lib64

      • R

        • library

          • qtl

            • BUGS.txt

            • CITATION

            • DESCRIPTION

            • INDEX

            • INSTALL_ME.txt

            • MQM-TODO.txt

            • Meta

              • Rd.rds

              • data.rds

              • features.rds

              • hsearch.rds

              • links.rds

              • nsInfo.rds

              • package.rds

              • vignette.rds

            • NAMESPACE

            • NEWS.md

            • R

              • qtl

              • qtl.rdb

              • qtl.rdx

            • data

              • badorder.RData

              • bristle3.RData

              • bristleX.RData

              • fake.4way.RData

              • fake.bc.RData

              • fake.f2.RData

              • hyper.RData

              • listeria.RData

              • locations.RData

              • map10.RData

              • mapthis.RData

              • multitrait.RData

            • doc

              • Sources

                • MQM

                  • MQM-tour.R

                  • MQM-tour.Rnw

                  • MQM-tour.tex

                  • SweaveIt.R

                  • SweaveIt.Rout

                  • mqm

                    • advantages_Rd.txt

                    • advantages_latex.txt

                    • description.txt

                    • limitations.txt

                    • parallelisation_references.txt

                    • significance_references.txt

                    • standard_example.txt

                    • standard_references.txt

                    • standard_seealso.txt

                  • sweaveit.bat

                  • sweaveit.sh

                • geneticmaps.Rnw

                • new_multiqtl.Rnw

                • new_summary_scanone.Rnw

                • new_summary_scantwo.Rnw

                • rqtltour.tex

                • rqtltour2.tex

              • bcsft.R

              • bcsft.Rnw

              • bcsft.pdf

              • geneticmaps.R

              • geneticmaps.pdf

              • index.html

              • new_multiqtl.R

              • new_multiqtl.pdf

              • new_summary_scanone.R

              • new_summary_scanone.pdf

              • new_summary_scantwo.R

              • new_summary_scantwo.pdf

              • rqtltour.R

              • rqtltour.pdf

              • rqtltour2.R

              • rqtltour2.pdf

            • help

              • AnIndex

              • aliases.rds

              • paths.rds

              • qtl.rdb

              • qtl.rdx

            • html

              • 00Index.html

              • MQM.html

              • R.css

              • a.starting.point.html

              • add.cim.covar.html

              • add.threshold.html

              • addcovarint.html

              • addint.html

              • addloctocross.html

              • addmarker.html

              • addpair.html

              • addqtl.html

              • addtoqtl.html

              • allchrsplits.html

              • argmax.geno.html

              • arithscan.html

              • arithscanperm.html

              • badorder.html

              • bayesint.html

              • bristle3.html

              • bristleX.html

              • c.cross.html

              • c.scanone.html

              • c.scanoneperm.html

              • c.scantwo.html

              • c.scantwoperm.html

              • calc.errorlod.html

              • calc.genoprob.html

              • calc.penalties.html

              • cbind.scanoneperm.html

              • cbind.scantwoperm.html

              • checkAlleles.html

              • chrlen.html

              • chrnames.html

              • cim.html

              • clean.cross.html

              • clean.scantwo.html

              • cleanGeno.html

              • comparecrosses.html

              • comparegeno.html

              • compareorder.html

              • condense.scantwo.html

              • convert.map.html

              • convert.scanone.html

              • convert.scantwo.html

              • convert2riself.html

              • convert2risib.html

              • convert2sa.html

              • countXO.html

              • drop.dupmarkers.html

              • drop.markers.html

              • drop.nullmarkers.html

              • dropfromqtl.html

              • droponemarker.html

              • effectplot.html

              • effectscan.html

              • est.map.html

              • est.rf.html

              • fake.4way.html

              • fake.bc.html

              • fake.f2.html

              • fill.geno.html

              • find.flanking.html

              • find.marker.html

              • find.markerpos.html

              • find.pheno.html

              • find.pseudomarker.html

              • findDupMarkers.html

              • find_large_intervals.html

              • findmarkerindex.html

              • fitqtl.html

              • fitstahl.html

              • flip.order.html

              • formLinkageGroups.html

              • formMarkerCovar.html

              • geno.crosstab.html

              • geno.image.html

              • geno.table.html

              • getid.html

              • groupclusteredheatmap.html

              • hyper.html

              • inferFounderHap.html

              • inferredpartitions.html

              • interpPositions.html

              • jittermap.html

              • listeria.html

              • locateXO.html

              • locations.html

              • lodint.html

              • makeqtl.html

              • map10.html

              • map2table.html

              • mapthis.html

              • markerlrt.html

              • markernames.html

              • max.scanPhyloQTL.html

              • max.scanone.html

              • max.scantwo.html

              • movemarker.html

              • mqmaugment.html

              • mqmautocofactors.html

              • mqmextractmarkers.html

              • mqmfind.marker.html

              • mqmgetmodel.html

              • mqmpermutation.html

              • mqmplotcircle.html

              • mqmplotcistrans.html

              • mqmplotclusteredheatmap.html

              • mqmplotcofactors.html

              • mqmplotdirectedqtl.html

              • mqmplotheatmap.html

              • mqmplotmultitrait.html

              • mqmplotpermutations.html

              • mqmplotsingletrait.html

              • mqmprocesspermutation.html

              • mqmscan.html

              • mqmscanall.html

              • mqmscanfdr.html

              • mqmsetcofactors.html

              • mqmtestnormal.html

              • multitrait.html

              • nchr.html

              • nind.html

              • nmar.html

              • nmissing.html

              • nphe.html

              • nqrank.html

              • nqtl.html

              • ntyped.html

              • nullmarkers.html

              • orderMarkers.html

              • phenames.html

              • pickMarkerSubset.html

              • plot.comparegeno.html

              • plot.cross.html

              • plot.errorlod.html

              • plot.geno.html

              • plot.info.html

              • plot.map.html

              • plot.missing.html

              • plot.pheno.html

              • plot.pxg.html

              • plot.qtl.html

              • plot.rf.html

              • plot.rfmatrix.html

              • plot.scanPhyloQTL.html

              • plot.scanone.html

              • plot.scanoneboot.html

              • plot.scanoneperm.html

              • plot.scantwo.html

              • plot.scantwoperm.html

              • plotLodProfile.html

              • plotModel.html

              • pull.argmaxgeno.html

              • pull.draws.html

              • pull.geno.html

              • pull.genoprob.html

              • pull.map.html

              • pull.markers.html

              • pull.pheno.html

              • pull.rf.html

              • qtl-internal.html

              • qtlversion.html

              • read.cross.html

              • readMWril.html

              • reduce2grid.html

              • refineqtl.html

              • reorderqtl.html

              • replace.map.html

              • replacemap.scanone.html

              • replacemap.scantwo.html

              • replaceqtl.html

              • rescalemap.html

              • ripple.html

              • scanPhyloQTL.html

              • scanone.html

              • scanoneboot.html

              • scanonevar.html

              • scanonevar.meanperm.html

              • scanonevar.varperm.html

              • scanqtl.html

              • scantwo.html

              • scantwopermhk.html

              • shiftmap.html

              • sim.cross.html

              • sim.geno.html

              • sim.map.html

              • simFounderSnps.html

              • simPhyloQTL.html

              • simulateMissingData.html

              • stepwiseqtl.html

              • strip.partials.html

              • subset.cross.html

              • subset.map.html

              • subset.scanone.html

              • subset.scanoneperm.html

              • subset.scantwo.html

              • subset.scantwoperm.html

              • summary.comparegeno.html

              • summary.cross.html

              • summary.fitqtl.html

              • summary.map.html

              • summary.qtl.html

              • summary.ripple.html

              • summary.scanPhyloQTL.html

              • summary.scanone.html

              • summary.scanoneboot.html

              • summary.scanoneperm.html

              • summary.scantwo.html

              • summary.scantwo.old.html

              • summary.scantwoperm.html

              • switch.order.html

              • switchAlleles.html

              • table2map.html

              • top.errorlod.html

              • totmar.html

              • transformPheno.html

              • tryallpositions.html

              • typingGap.html

              • write.cross.html

              • xaxisloc.scanone.html

            • libs

              • qtl.so

            • sampledata

              • README.txt

              • gen.txt

              • listeria.csv

              • listeria.qtx

              • listeria_gen.csv

              • listeria_gen_rot.csv

              • listeria_map.txt

              • listeria_maps.txt

              • listeria_phe.csv

              • listeria_phe_rot.csv

              • listeria_qc_cro.txt

              • listeria_qc_map.txt

              • listeria_raw.txt

              • listeria_rot.csv

              • map.txt

              • phe.txt