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
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.cross	plot.cross
plot.errorlod	plot.errorlod
plot.geno	plot.geno
plot.info	plot.info
plot.map	plot.map
plot.missing	plot.missing
plot.pheno	plot.pheno
plot.pxg	plot.pxg
plot.qtl	plot.qtl
plot.rf	plot.rf
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.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.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
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
