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MQM.Rd
a.starting.point.Rd
add.cim.covar.Rd
add.threshold.Rd
addcovarint.Rd
addint.Rd
addloctocross.Rd
addpair.Rd
addqtl.Rd
addtoqtl.Rd
allchrsplits.Rd
argmax.geno.Rd
arithscan.Rd
arithscanperm.Rd
badorder.Rd
bayesint.Rd
bristle3.Rd
bristleX.Rd
c.cross.Rd
c.scanone.Rd
c.scanoneperm.Rd
c.scantwo.Rd
c.scantwoperm.Rd
calc.errorlod.Rd
calc.genoprob.Rd
calc.penalties.Rd
cbind.scanoneperm.Rd
checkAlleles.Rd
chrlen.Rd
chrnames.Rd
cim.Rd
clean.cross.Rd
clean.scantwo.Rd
cleanGeno.Rd
comparecrosses.Rd
comparegeno.Rd
compareorder.Rd
condense.scantwo.Rd
convert.map.Rd
convert.scanone.Rd
convert.scantwo.Rd
convert2riself.Rd
convert2risib.Rd
convert2sa.Rd
countXO.Rd
drop.dupmarkers.Rd
drop.markers.Rd
drop.nullmarkers.Rd
dropfromqtl.Rd
droponemarker.Rd
effectplot.Rd
effectscan.Rd
est.map.Rd
est.rf.Rd
fake.4way.Rd
fake.bc.Rd
fake.f2.Rd
fill.geno.Rd
find.flanking.Rd
find.marker.Rd
find.markerpos.Rd
find.pheno.Rd
find.pseudomarker.Rd
findDupMarkers.Rd
findmarkerindex.Rd
fitqtl.Rd
fitstahl.Rd
formLinkageGroups.Rd
geno.crosstab.Rd
geno.image.Rd
geno.table.Rd
getid.Rd
groupclusteredheatmap.Rd
hyper.Rd
inferFounderHap.Rd
inferredpartitions.Rd
interpPositions.Rd
jittermap.Rd
listeria.Rd
locateXO.Rd
locations.Rd
lodint.Rd
makeqtl.Rd
map10.Rd
mapthis.Rd
markerlrt.Rd
markernames.Rd
max.scanPhyloQTL.Rd
max.scanone.Rd
max.scantwo.Rd
movemarker.Rd
mqmaugment.Rd
mqmautocofactors.Rd
mqmextractmarkers.Rd
mqmfind.marker.Rd
mqmgetmodel.Rd
mqmpermutation.Rd
mqmplotcircle.Rd
mqmplotcistrans.Rd
mqmplotclusteredheatmap.Rd
mqmplotcofactors.Rd
mqmplotdirectedqtl.Rd
mqmplotheatmap.Rd
mqmplotmultitrait.Rd
mqmplotpermutations.Rd
mqmplotsingletrait.Rd
mqmprocesspermutation.Rd
mqmscan.Rd
mqmscanall.Rd
mqmscanfdr.Rd
mqmsetcofactors.Rd
mqmtestnormal.Rd
multitrait.Rd
nchr.Rd
nind.Rd
nmar.Rd
nmissing.Rd
nphe.Rd
nqrank.Rd
ntyped.Rd
nullmarkers.Rd
orderMarkers.Rd
phenames.Rd
pickMarkerSubset.Rd
plot.cross.Rd
plot.errorlod.Rd
plot.geno.Rd
plot.info.Rd
plot.map.Rd
plot.missing.Rd
plot.pheno.Rd
plot.pxg.Rd
plot.qtl.Rd
plot.rf.Rd
plot.rfmatrix.Rd
plot.scanPhyloQTL.Rd
plot.scanone.Rd
plot.scanoneboot.Rd
plot.scanoneperm.Rd
plot.scantwo.Rd
plot.scantwoperm.Rd
plotLodProfile.Rd
plotModel.Rd
pull.argmaxgeno.Rd
pull.draws.Rd
pull.geno.Rd
pull.genoprob.Rd
pull.map.Rd
pull.markers.Rd
pull.pheno.Rd
pull.rf.Rd
qtl-internal.Rd
qtlversion.Rd
read.cross.Rd
readMWril.Rd
refineqtl.Rd
reorderqtl.Rd
replace.map.Rd
replacemap.scanone.Rd
replacemap.scantwo.Rd
replaceqtl.Rd
rescalemap.Rd
ripple.Rd
scanPhyloQTL.Rd
scanone.Rd
scanoneboot.Rd
scanqtl.Rd
scantwo.Rd
shiftmap.Rd
sim.cross.Rd
sim.geno.Rd
sim.map.Rd
simFounderSnps.Rd
simPhyloQTL.Rd
simulateMissingData.Rd
stepwiseqtl.Rd
strip.partials.Rd
subset.cross.Rd
subset.map.Rd
subset.scanone.Rd
subset.scanoneperm.Rd
subset.scantwo.Rd
subset.scantwoperm.Rd
summary.cross.Rd
summary.fitqtl.Rd
summary.map.Rd
summary.qtl.Rd
summary.ripple.Rd
summary.scanPhyloQTL.Rd
summary.scanone.Rd
summary.scanoneboot.Rd
summary.scanoneperm.Rd
summary.scantwo.Rd
summary.scantwo.old.Rd
summary.scantwoperm.Rd
switch.order.Rd
switchAlleles.Rd
top.errorlod.Rd
totmar.Rd
transformPheno.Rd
tryallpositions.Rd
typingGap.Rd
write.cross.Rd
xaxisloc.scanone.Rd
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