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
DGLM_norm Source code
LikePheVector Source code
MQM Man page
[.cross Man page
[.map Man page
[.scanoneperm Man page
[.scantwoperm Man page
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
c.scantwo Man page
c.scantwoperm Man page
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
checkcovar Man page Source code
checkdistances Source code
checkformula Man page Source code
chrlen Man page Source code
chrnames Man page 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
deparseQTLformula Man page Source code
discan Source code
drawcirculargenome Source code
drawspline 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 Source code
effectplot.calmeanse Source code
effectplot.getmark 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
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
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
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.cross Man page Source code
plot.effectscan Source code
plot.errorlod Man page
plot.geno Man page
plot.info Man page
plot.map Man page
plot.missing Man page
plot.pheno Man page
plot.pxg Man page
plot.qtl Man page Source code
plot.rf Man page
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
plotGeno Man page
plotInfo Man page
plotLodProfile Man page Source code
plotMap Man page
plotMissing Man page
plotModel Man page Source code
plotPXG Man page
plotPheno Man page
plotRF Man page
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.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.cro.qtlcart Source code
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.qtlcart Source code
read.cross.qtx Source code
read.cross.tidy Source code
read.map.qtlcart 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
roundqtlpos 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 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.cross Man page Source code
summary.fitqtl Man page Source code
summary.map Man page
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 Source code
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
qtl documentation built on June 20, 2017, 9:05 a.m.