API for qtl
Tools for Analyzing QTL Experiments

Global functions
+.scanone	Man page
+.scanoneperm	Man page
+.scantwo	Man page
+.scantwoperm	Man page
-.scanone	Man page
-.scanoneperm	Man page
-.scantwo	Man page
-.scantwoperm	Man page
.scantwopermhk	Source code
DGLM_norm	Source code
LikePheVector	Source code
MQM	Man page
[.cross	Man page
[.map	Man page
[.scanoneperm	Man page
[.scantwoperm	Man page
`[.cross`	Source code
`[.map`	Source code
`[.scanoneperm`	Source code
`[.scantwoperm`	Source code
add.cim.covar	Man page Source code
add.threshold	Man page Source code
addcovarint	Man page Source code
addint	Man page Source code
addloctocross	Man page Source code
addmarker	Man page Source code
addmarkerstointervalmap	Man page Source code
addpair	Man page Source code
addqtl	Man page Source code
addtoqtl	Man page Source code
adjust.rf.ri	Source code
allchrsplits	Man page Source code
argmax.geno	Man page Source code
asnumericwithdec	Source code
badorder	Man page
bayesint	Man page Source code
bristle3	Man page
bristleX	Man page
c.cross	Man page Source code
c.scanone	Man page Source code
c.scanoneperm	Man page Source code
c.scantwo	Man page Source code
c.scantwoperm	Man page Source code
calc.errorlod	Man page Source code
calc.genoprob	Man page Source code
calc.genoprob.special	Source code
calc.pairprob	Source code
calc.penalties	Man page Source code
calc.penalties.X	Source code
calc.plod	Man page Source code
calc.plod.X	Source code
calcPermPval	Source code
calculatedensity	Source code
cbind.scanone	Man page
cbind.scanoneperm	Man page Source code
cbind.scantwo	Man page
cbind.scantwoperm	Man page Source code
charround	Source code
checkAlleles	Man page Source code
checkPhyloCrosses	Source code
checkPhyloPartition	Source code
checkStepwiseqtlStart	Man page Source code
check_colindex	Source code
check_rowindex	Source code
checkcovar	Man page Source code
checkdistances	Source code
checkformula	Man page Source code
chrlen	Man page Source code
chrnames	Man page Source code
chrtype	Source code
cim	Man page Source code
circlelocations	Source code
clean	Man page Source code
clean.cross	Man page Source code
clean.scantwo	Man page Source code
cleanGeno	Man page Source code
comparecrosses	Man page Source code
comparegeno	Man page Source code
compareorder	Man page Source code
condense	Man page Source code
condense.scantwo	Man page Source code
convert	Man page Source code
convert.map	Man page Source code
convert.scanone	Man page Source code
convert.scantwo	Man page Source code
convert2bcsft	Man page Source code
convert2riself	Man page Source code
convert2risib	Man page Source code
convert2sa	Man page Source code
convertMWril	Source code
countXO	Man page Source code
countqtlterms	Man page Source code
countqtltermsX	Source code
create.map	Man page Source code
crosstype	Source code
deparseQTLformula	Man page Source code
discan	Source code
drawcirculargenome	Source code
drop.dupmarkers	Man page Source code
drop.markers	Man page Source code
drop.nullmarkers	Man page Source code
dropXcol	Source code
dropfromqtl	Man page Source code
dropfromqtlformula	Source code
droponemarker	Man page Source code
effectplot	Man page
effectplot.calmeanse	Source code
effectscan	Man page Source code
est.map	Man page Source code
est.rf	Man page Source code
estimatemarkerlod	Source code
expandf2covar	Source code
fake.4way	Man page
fake.bc	Man page
fake.f2	Man page
fill.geno	Man page Source code
find.flanking	Man page Source code
find.marker	Man page Source code
find.markerindex	Man page Source code
find.markerpos	Man page Source code
find.pheno	Man page Source code
find.pseudomarker	Man page Source code
find.pseudomarkerpos	Man page Source code
findDupMarkers	Man page Source code
find_large_intervals	Man page Source code
fitqtl	Man page Source code
fitqtlengine	Man page Source code
fitstahl	Man page Source code
fitstahl.este	Source code
fitstahl.este.sub	Source code
fitstahl.estp	Source code
fitstahl.estp.sub	Source code
fitstahl.estpe	Source code
fitstahl.estpe.sub	Source code
fixX4write	Source code
fixXgeno.bc	Source code
fixXgeno.f2	Source code
flip.order	Man page Source code
flipcross	Man page Source code
force_sexstrata	Source code
formLinkageGroups	Man page Source code
formMarkerCovar	Man page Source code
genAllPartitions	Man page Source code
geno.crosstab	Man page Source code
geno.image	Man page Source code
geno.table	Man page Source code
genotab.em	Source code
get.indID.for.qtab	Source code
get.phenotype.type	Source code
get.qtab.geno.symbols	Source code
get.qtlHD.ID	Source code
getChr	Source code
getThird	Source code
getchromosomelength	Source code
getgenomelength	Source code
getgenonames	Man page Source code
getgenonames.for.qtab	Source code
getid	Man page Source code
getsex	Man page Source code
grab.arg.names	Source code
groupclusteredheatmap	Man page Source code
hyper	Man page
imf.cf	Man page Source code
imf.h	Man page Source code
imf.k	Man page Source code
imf.m	Man page Source code
imf.stahl	Man page Source code
inferFounderHap	Man page Source code
inferredpartitions	Man page Source code
interpPositions	Man page Source code
interpmap	Source code
interpmap4scantwo	Source code
jittermap	Man page Source code
listeria	Man page
locateXO	Man page Source code
locatemarker	Man page Source code
locations	Man page
locationtocircle	Source code
lodint	Man page Source code
loopthroughmulti	Source code
makeSSmap	Source code
make_unique	Source code
makeqtl	Man page Source code
map10	Man page
map2table	Man page Source code
mapthis	Man page
markerforwsel	Source code
markerforwself2	Source code
markerloglik	Source code
markerlrt	Man page Source code
markernames	Man page Source code
matchchr	Man page Source code
max.scanPhyloQTL	Man page Source code
max.scanone	Man page Source code
max.scantwo	Man page Source code
max.scantwocondensed	Man page
mf.cf	Man page Source code
mf.h	Man page Source code
mf.k	Man page Source code
mf.m	Man page Source code
mf.stahl	Man page Source code
movemarker	Man page Source code
mq_grab_param	Source code
mqm_version	Man page Source code
mqmaugment	Man page Source code
mqmaugment_on_cofactors	Source code
mqmautocofactors	Man page Source code
mqmextractmarkers	Man page Source code
mqmextractpseudomarkers	Source code
mqmfind.marker	Man page Source code
mqmgetmodel	Man page Man page Source code
mqmpermutation	Man page Source code
mqmplot.circle	Man page Source code
mqmplot.cistrans	Man page Source code
mqmplot.clusteredheatmap	Man page Source code
mqmplot.cofactors	Man page Source code
mqmplot.directedqtl	Man page Source code
mqmplot.heatmap	Man page Source code
mqmplot.multitrait	Man page Source code
mqmplot.permutations	Man page Source code
mqmplot.singletrait	Man page Source code
mqmprocesspermutation	Man page Source code
mqmscan	Man page Source code
mqmscanall	Man page Source code
mqmscanfdr	Man page Source code
mqmsetcofactors	Man page Source code
mqmtestnormal	Man page Source code
multitrait	Man page
mybinaryrep	Source code
nchr	Man page Source code
nind	Man page Source code
nmar	Man page Source code
nmissing	Man page Source code
nphe	Man page Source code
nqrank	Man page Source code
nqtl	Man page Source code
ntyped	Man page Source code
nullmarkers	Man page Source code
omit_x_chr	Source code
orderMarkers	Man page Source code
orderMarkers.sub	Source code
ourline	Source code
ourstop	Source code
parseformula	Man page Source code
phenames	Man page Source code
pickMarkerSubset	Man page Source code
plot.comparegeno	Man page Source code
plot.cross	Man page
plot.effectscan	Source code
plot.map	Man page Source code
plot.qtl	Man page Source code
plot.rfmatrix	Man page Source code
plot.scanPhyloQTL	Man page Source code
plot.scanone	Man page Source code
plot.scanoneboot	Man page Source code
plot.scanoneperm	Man page Source code
plot.scantwo	Man page Source code
plot.scantwoperm	Man page Source code
plotErrorlod	Man page Source code
plotGeno	Man page Source code
plotInfo	Man page Source code
plotLodProfile	Man page Source code
plotMap	Man page
plotMissing	Man page Source code
plotModel	Man page Source code
plotPXG	Man page Source code
plotPheno	Man page Source code
plotRF	Man page Source code
polyplot	Man page Source code
print.addcovarint	Man page Source code
print.addint	Man page Source code
print.compactqtl	Man page Source code
print.cross	Man page Source code
print.map	Man page Source code
print.qtl	Man page Source code
print.scanoneboot	Man page Source code
print.scantwo	Man page Source code
print.summary.addpair	Man page Source code
print.summary.compactqtl	Man page Source code
print.summary.comparegeno	Man page Source code
print.summary.cross	Man page Source code
print.summary.fitqtl	Man page Source code
print.summary.map	Man page Source code
print.summary.qtl	Man page Source code
print.summary.ripple	Man page Source code
print.summary.scanone	Man page Source code
print.summary.scanoneperm	Man page Source code
print.summary.scantwo	Man page Source code
print.summary.scantwo.old	Man page Source code
print.summary.scantwoperm	Man page Source code
printQTLformulanicely	Source code
pull.argmaxgeno	Man page Source code
pull.draws	Man page Source code
pull.geno	Man page Source code
pull.genoprob	Man page Source code
pull.map	Man page Source code
pull.markers	Man page Source code
pull.pheno	Man page Source code
pull.rf	Man page Source code
qtl-package	Man page
qtlByPartition	Source code
qtlformulasymmetric	Source code
qtlversion	Man page Source code
rbind.scanoneperm	Man page
rbind.scantwoperm	Man page
read.cross	Man page Source code
read.cross.bcsft	Source code
read.cross.csv	Source code
read.cross.csvs	Source code
read.cross.gary	Source code
read.cross.karl	Source code
read.cross.mm	Source code
read.cross.mq	Source code
read.cross.mq.loc	Source code
read.cross.mq.map	Source code
read.cross.mq.qua	Source code
read.cross.qtx	Source code
read.cross.tidy	Source code
read.maps.mm	Source code
readMWril	Man page Source code
reduce2grid	Man page Source code
refineqtl	Man page Source code
reorderqtl	Man page Source code
reorgRIargmax	Source code
reorgRIdraws	Source code
reorgRIgenoprob	Source code
reorgRIpairprob	Source code
replace.map	Man page Source code
replacemap	Man page Source code
replacemap.cross	Man page Source code
replacemap.scanone	Man page Source code
replacemap.scantwo	Man page Source code
replaceqtl	Man page Source code
rescalemap	Man page Source code
restoreMWrilGeno	Source code
reviseXdata	Man page Source code
revisecovar	Source code
reviseqtlnuminformula	Man page Source code
ripple	Man page Source code
ripple.perm.sub	Source code
ripple.perm1	Source code
ripple.perm2	Source code
rippleSnowCountxo	Source code
rippleSnowLik	Source code
rqtl.to.qtab.founder	Source code
rqtl.to.qtab.genotypes	Source code
rqtl.to.qtab.location	Source code
rqtl.to.qtab.phenotypes	Source code
rqtl.to.qtab.symbols	Source code
scanPhyloQTL	Man page Source code
scanall	Man page Source code
scanone	Man page Source code
scanone.perm	Source code
scanone.perm.engine	Source code
scanoneXnull	Source code
scanoneboot	Man page Source code
scanonevar	Man page Source code
scanonevar.meanperm	Man page Source code
scanonevar.varperm	Man page Source code
scanqtl	Man page Source code
scantwo	Man page Source code
scantwo.perm	Source code
scantwo.perm.engine	Source code
scantwoperm2scanoneperm	Source code
scantwopermhk	Man page Source code
scoremissingmarkers	Source code
shiftmap	Man page Source code
sim.bcg	Source code
sim.cross	Man page Source code
sim.cross.4way	Source code
sim.cross.bc	Source code
sim.cross.bcsft	Source code
sim.cross.f2	Source code
sim.geno	Man page Source code
sim.map	Man page Source code
sim.ril	Source code
simFounderSnps	Man page Source code
simPhyloQTL	Man page Source code
simulatemissingdata	Man page Source code
snowCoreALL	Source code
snowCoreBOOT	Source code
sortPhyloPartitions	Source code
stepsize	Source code
stepwiseqtl	Man page Source code
stepwiseqtlX	Source code
stringPhenoToInt	Source code
strip.partials	Man page Source code
subrousummaryscantwo	Man page Source code
subset.cross	Man page Source code
subset.map	Man page Source code
subset.scanone	Man page Source code
subset.scanoneperm	Man page Source code
subset.scantwo	Man page Source code
subset.scantwoperm	Man page Source code
summary.addcovarint	Man page Source code
summary.addint	Man page Source code
summary.compactqtl	Man page Source code
summary.comparegeno	Man page Source code
summary.cross	Man page Source code
summary.fitqtl	Man page Source code
summary.map	Man page Source code
summary.qtl	Man page Source code
summary.ripple	Man page Source code
summary.scanPhyloQTL	Man page Source code
summary.scanone	Man page Source code
summary.scanoneboot	Man page Source code
summary.scanoneperm	Man page Source code
summary.scantwo	Man page Source code
summary.scantwocondensed	Man page
summary.scantwoperm	Man page Source code
summaryMap	Man page
summaryScantwoOld	Man page
sw2numeric	Source code
switch.order	Man page Source code
switchAlleles	Man page Source code
table2map	Man page Source code
testchr	Source code
top.errorlod	Man page Source code
totmar	Man page Source code
transformPheno	Man page Source code
tryallpositions	Man page Source code
typingGap	Man page Source code
updateParallelRNG	Source code
vbscan	Source code
viridis_qtl	Source code
write.cross	Man page Source code
write.cross.csv	Source code
write.cross.gary	Source code
write.cross.mm	Source code
write.cross.mq	Source code
write.cross.mq.loc	Source code
write.cross.mq.map	Source code
write.cross.mq.qua	Source code
write.cross.qtab	Source code
write.cross.qtlcart	Source code
write.cross.tidy	Source code
xaxisloc.scanone	Man page Source code