EVOLUTION-MANAGER

Edit File: AnIndex

qtl-package a.starting.point +.scanone arithscan +.scanoneperm arithscanperm +.scantwo arithscan +.scantwoperm arithscanperm -.scanone arithscan -.scanoneperm arithscanperm -.scantwo arithscan -.scantwoperm arithscanperm add.cim.covar add.cim.covar add.threshold add.threshold addcovarint addcovarint addint addint addloctocross addloctocross addmarker addmarker addmarkerstointervalmap qtl-internal addpair addpair addqtl addqtl addtoqtl addtoqtl allchrsplits allchrsplits argmax.geno argmax.geno badorder badorder bayesint bayesint bristle3 bristle3 bristleX bristleX c.cross c.cross c.scanone c.scanone c.scanoneperm c.scanoneperm c.scantwo c.scantwo c.scantwoperm c.scantwoperm calc.errorlod calc.errorlod calc.genoprob calc.genoprob calc.penalties calc.penalties calc.plod qtl-internal cbind.scanone c.scanone cbind.scanoneperm cbind.scanoneperm cbind.scantwo c.scantwo cbind.scantwoperm cbind.scantwoperm checkAlleles checkAlleles checkcovar qtl-internal checkformula qtl-internal checkStepwiseqtlStart qtl-internal chrlen chrlen chrnames chrnames cim cim clean qtl-internal clean.cross clean.cross clean.scantwo clean.scantwo cleanGeno cleanGeno comparecrosses comparecrosses comparegeno comparegeno compareorder compareorder condense qtl-internal condense.scantwo condense.scantwo convert qtl-internal convert.map convert.map convert.scanone convert.scanone convert.scantwo convert.scantwo convert2bcsft qtl-internal convert2riself convert2riself convert2risib convert2risib convert2sa convert2sa countqtlterms qtl-internal countXO countXO create.map qtl-internal deparseQTLformula qtl-internal drop.dupmarkers drop.dupmarkers drop.markers drop.markers drop.nullmarkers drop.nullmarkers dropfromqtl dropfromqtl droponemarker droponemarker effectplot effectplot effectscan effectscan est.map est.map est.rf est.rf fake.4way fake.4way fake.bc fake.bc fake.f2 fake.f2 fill.geno fill.geno find.flanking find.flanking find.marker find.marker find.markerindex findmarkerindex find.markerpos find.markerpos find.pheno find.pheno find.pseudomarker find.pseudomarker find.pseudomarkerpos qtl-internal findDupMarkers findDupMarkers find_large_intervals find_large_intervals fitqtl fitqtl fitqtlengine qtl-internal fitstahl fitstahl flip.order flip.order flipcross qtl-internal formLinkageGroups formLinkageGroups formMarkerCovar formMarkerCovar genAllPartitions qtl-internal geno.crosstab geno.crosstab geno.image geno.image geno.table geno.table getgenonames qtl-internal getid getid getsex qtl-internal groupclusteredheatmap groupclusteredheatmap hyper hyper imf.cf qtl-internal imf.h qtl-internal imf.k qtl-internal imf.m qtl-internal imf.stahl qtl-internal inferFounderHap inferFounderHap inferredpartitions inferredpartitions interpPositions interpPositions jittermap jittermap listeria listeria locatemarker qtl-internal locateXO locateXO locations locations lodint lodint makeqtl makeqtl map10 map10 map2table map2table mapthis mapthis markerlrt markerlrt markernames markernames matchchr qtl-internal max.scanone max.scanone max.scanPhyloQTL max.scanPhyloQTL max.scantwo max.scantwo max.scantwocondensed qtl-internal mf.cf qtl-internal mf.h qtl-internal mf.k qtl-internal mf.m qtl-internal mf.stahl qtl-internal movemarker movemarker MQM MQM mqmaugment mqmaugment mqmautocofactors mqmautocofactors mqmextractmarkers mqmextractmarkers mqmfind.marker mqmfind.marker mqmgetmodel mqmgetmodel mqmpermutation mqmpermutation mqmplot.circle mqmplotcircle mqmplot.cistrans mqmplotcistrans mqmplot.clusteredheatmap mqmplotclusteredheatmap mqmplot.cofactors mqmplotcofactors mqmplot.directedqtl mqmplotdirectedqtl mqmplot.heatmap mqmplotheatmap mqmplot.multitrait mqmplotmultitrait mqmplot.permutations mqmplotpermutations mqmplot.singletrait mqmplotsingletrait mqmprocesspermutation mqmprocesspermutation mqmscan mqmscan mqmscanall mqmscanall mqmscanfdr mqmscanfdr mqmsetcofactors mqmsetcofactors mqmtestnormal mqmtestnormal mqm_version qtl-internal multitrait multitrait nchr nchr nind nind nmar nmar nmissing nmissing nphe nphe nqrank nqrank nqtl nqtl ntyped ntyped nullmarkers nullmarkers orderMarkers orderMarkers parseformula qtl-internal phenames phenames pickMarkerSubset pickMarkerSubset plot.comparegeno plot.comparegeno plot.cross plot.cross plot.map plot.map plot.qtl plot.qtl plot.rfmatrix plot.rfmatrix plot.scanone plot.scanone plot.scanoneboot plot.scanoneboot plot.scanoneperm plot.scanoneperm plot.scanPhyloQTL plot.scanPhyloQTL plot.scantwo plot.scantwo plot.scantwoperm plot.scantwoperm plotErrorlod plot.errorlod plotGeno plot.geno plotInfo plot.info plotLodProfile plotLodProfile plotMap plot.map plotMissing plot.missing plotModel plotModel plotPheno plot.pheno plotPXG plot.pxg plotRF plot.rf polyplot qtl-internal print.addcovarint qtl-internal print.addint qtl-internal print.compactqtl qtl-internal print.cross qtl-internal print.map qtl-internal print.qtl qtl-internal print.scanoneboot qtl-internal print.scantwo qtl-internal print.summary.addpair qtl-internal print.summary.compactqtl qtl-internal print.summary.comparegeno qtl-internal print.summary.cross qtl-internal print.summary.fitqtl qtl-internal print.summary.map qtl-internal print.summary.qtl qtl-internal print.summary.ripple qtl-internal print.summary.scanone qtl-internal print.summary.scanoneperm qtl-internal print.summary.scantwo qtl-internal print.summary.scantwo.old qtl-internal print.summary.scantwoperm qtl-internal pull.argmaxgeno pull.argmaxgeno pull.draws pull.draws pull.geno pull.geno pull.genoprob pull.genoprob pull.map pull.map pull.markers pull.markers pull.pheno pull.pheno pull.rf pull.rf qtlversion qtlversion rbind.scanoneperm c.scanoneperm rbind.scantwoperm c.scantwoperm read.cross read.cross readMWril readMWril reduce2grid reduce2grid refineqtl refineqtl reorderqtl reorderqtl replace.map replace.map replacemap qtl-internal replacemap.cross replace.map replacemap.scanone replacemap.scanone replacemap.scantwo replacemap.scantwo replaceqtl replaceqtl rescalemap rescalemap reviseqtlnuminformula qtl-internal reviseXdata qtl-internal ripple ripple scanall qtl-internal scanone scanone scanoneboot scanoneboot scanonevar scanonevar scanonevar.meanperm scanonevar.meanperm scanonevar.varperm scanonevar.varperm scanPhyloQTL scanPhyloQTL scanqtl scanqtl scantwo scantwo scantwopermhk scantwopermhk shiftmap shiftmap sim.cross sim.cross sim.geno sim.geno sim.map sim.map simFounderSnps simFounderSnps simPhyloQTL simPhyloQTL simulatemissingdata simulateMissingData stepwiseqtl stepwiseqtl strip.partials strip.partials subrousummaryscantwo qtl-internal subset.cross subset.cross subset.map subset.map subset.scanone subset.scanone subset.scanoneperm subset.scanoneperm subset.scantwo subset.scantwo subset.scantwoperm subset.scantwoperm summary.addcovarint qtl-internal summary.addint qtl-internal summary.compactqtl qtl-internal summary.comparegeno summary.comparegeno summary.cross summary.cross summary.fitqtl summary.fitqtl summary.map summary.map summary.qtl summary.qtl summary.ripple summary.ripple summary.scanone summary.scanone summary.scanoneboot summary.scanoneboot summary.scanoneperm summary.scanoneperm summary.scanPhyloQTL summary.scanPhyloQTL summary.scantwo summary.scantwo summary.scantwocondensed qtl-internal summary.scantwoperm summary.scantwoperm summaryMap summary.map summaryScantwoOld summary.scantwo.old switch.order switch.order switchAlleles switchAlleles table2map table2map top.errorlod top.errorlod totmar totmar transformPheno transformPheno tryallpositions tryallpositions typingGap typingGap write.cross write.cross xaxisloc.scanone xaxisloc.scanone [.cross subset.cross [.map subset.map [.scanoneperm subset.scanoneperm [.scantwoperm subset.scantwoperm