add.to.population	add.to.population
add.to.populationSub.internal	add.to.population
add.to.populationSubAnnots.internal	phenotypes2genotypes-internal
add.to.populationSubGeno.internal	phenotypes2genotypes-internal
add.to.populationSubMap.internal	phenotypes2genotypes-internal
add.to.populationSubPheno.internal	phenotypes2genotypes-internal
analyseLineVariance	phenotypes2genotypes-internal
applyFunctionToFile	phenotypes2genotypes-internal
ascendingMaptoJigSawMap	phenotypes2genotypes-internal
assignChrToMarkers	assignedChrToMarkers
assignLinkageGroups	phenotypes2genotypes-internal
assignMaximum	cross.denovo
assignMaximumNoConflicts	cross.denovo
avg_map_distances	map.functions
bestCorelated.internal	phenotypes2genotypes-internal
bestCorelatedSub.internal	phenotypes2genotypes-internal
bestQTL.internal	phenotypes2genotypes-internal
bestQTLSub.internal	phenotypes2genotypes-internal
check.population	phenotypes2genotypes-internal
checkAndBind	phenotypes2genotypes-internal
checkForEpistasis	phenotypes2genotypes-internal
chromosomesLengths.internal	phenotypes2genotypes-internal
cleanGeno.internal	phenotypes2genotypes-internal
cleanNames.internal	phenotypes2genotypes-internal
cleanRfs	phenotypes2genotypes-internal
coloringMode	plotMapComparison
convertMap.internal	phenotypes2genotypes-internal
convertType.internal	phenotypes2genotypes-internal
create.population	create.population
createMix	phenotypes2genotypes-internal
createMix.test	phenotypes2genotypes-internal
cross.denovo	cross.denovo
cross.denovo.internal	phenotypes2genotypes-internal
cross.saturate	cross.saturate
dataObject	add.to.population
dataType	add.to.population
defaultCheck.internal	phenotypes2genotypes-internal
doCleanUp.internal	phenotypes2genotypes-internal
donothing	phenotypes2genotypes-internal
fake.population	fake.population
fakeFounders.internal	phenotypes2genotypes-internal
fakeMixUps.internal	phenotypes2genotypes-internal
fakePheno.internal	phenotypes2genotypes-internal
fakePhysicalMap.internal	phenotypes2genotypes-internal
filterRow.internal	phenotypes2genotypes-internal
find.diff.expressed	findDiffExpressed
find.mixups	find.mixups
findUsingTTest.internal	phenotypes2genotypes-internal
fullScanRow.internal	phenotypes2genotypes-internal
generate.biomarkers	generate.biomarkers
generate.biomarkers.internal	phenotypes2genotypes-internal
genotypeCheck.internal	phenotypes2genotypes-internal
genotypesToCross.internal	phenotypes2genotypes-internal
getChrOffsets.internal	phenotypes2genotypes-internal
getChromosome.internal	phenotypes2genotypes-internal
getMarkerOffsets	phenotypes2genotypes-internal
getMarkerOffsets.internal	phenotypes2genotypes-internal
getMarkerOffsetsFromMap	phenotypes2genotypes-internal
getpeaks.internal	phenotypes2genotypes-internal
getPopulationOffsets.internal	phenotypes2genotypes-internal
getYLocs.internal	phenotypes2genotypes-internal
groupLabels	findDiffExpressed
inListCheck.internal	phenotypes2genotypes-internal
inRangeCheck.internal	phenotypes2genotypes-internal
insertMarkers.internal	phenotypes2genotypes-internal
invertChromosome.internal	phenotypes2genotypes-internal
is.integer0	phenotypes2genotypes-internal
logarithmic	plotMarkerDistribution
lowerTrng.internal	phenotypes2genotypes-internal
majorityCorrelation	cross.denovo
majorityOfMarkers	cross.denovo
makeChromPal.internal	phenotypes2genotypes-internal
makeHaplos.internal	phenotypes2genotypes-internal
map2mapCorrelationMatrix	phenotypes2genotypes-internal
map2mapImage	phenotypes2genotypes-internal
mapMarkers.internal	phenotypes2genotypes-internal
map_distances	map.functions
margin	generate.biomarkers
markerPlacementPlot	markerPlacementPlot
markers	plotChildrenExpression
markersCorPlot	markersCorPlot
matchMarkers	phenotypes2genotypes-internal
meanCorrelation	cross.denovo
mergeChromosomes.internal	phenotypes2genotypes-internal
mergeEnv.internal	phenotypes2genotypes-internal
mergeInverted	phenotypes2genotypes-internal
mlog	phenotypes2genotypes-internal
mlogit	phenotypes2genotypes-internal
mprobit	phenotypes2genotypes-internal
msqrt	phenotypes2genotypes-internal
normalModeReading	phenotypes2genotypes-internal
numericCheck.internal	phenotypes2genotypes-internal
overlapInd	generate.biomarkers
pheno2geno	phenotypes2genotypes-package
phenotypeRow	plotMarkerDistribution
plot4Nmixture	phenotypes2genotypes-internal
plotChildrenExpression	plotChildrenExpression
plotMapComparison	plotMapComparison
plotMarkerDistribution	plotMarkerDistribution
plotParentalExpression	plotParentalExpression
plotRPpval	RPpval
population	create.population
power.plot	power.plot
print.population	phenotypes2genotypes-internal
printGeno.internal	phenotypes2genotypes-internal
processInteractions	phenotypes2genotypes-internal
projectOldMarkers	projectOldMarkers
proportion	generate.biomarkers
pull.biomarkers	pull.biomarkers
qtl.comparison.plot	qtl.comparison.plot
read.population	read.population
readSingleFile	phenotypes2genotypes-internal
rearrangeMarkers	phenotypes2genotypes-internal
reciproce	phenotypes2genotypes-internal
reduceChromosomesNumber	changeChromNumber
removeChromosomes	changeChromNumber
removeChromosomesSub.internal	phenotypes2genotypes-internal
removeTooSmallChromosomes	changeChromNumber
reorganizeMarkersWithin	reorganizeMarkersWithin
save.gff	save.gff
scan.qtls	scan.qtls
scoreMixups.internal	phenotypes2genotypes-internal
selectByLine	phenotypes2genotypes-internal
selectByLineApply	phenotypes2genotypes-internal
selectChr	phenotypes2genotypes-internal
selectPhenotypes	phenotypes2genotypes-internal
selectTopMarker.internal	phenotypes2genotypes-internal
set.geno.from.cross	set.geno.from.cross
showRPpval	RPpval
simBC.internal	phenotypes2genotypes-internal
simulateParentalPhenotypes	phenotypes2genotypes-internal
splitPheno.Apply	phenotypes2genotypes-internal
splitPheno.internal	phenotypes2genotypes-internal
splitPhenoRowEM.internal	phenotypes2genotypes-internal
sumMajorityCorrelation	cross.denovo
switchChromosomes.internal	phenotypes2genotypes-internal
testCross	testCross
testPopulation	testPopulation
transformation	transformations
tTestByLine	phenotypes2genotypes-internal
tTestByLineApply	phenotypes2genotypes-internal
twoGenosModel	phenotypes2genotypes-internal
write.population	write.population
writeGenotypes.internal	phenotypes2genotypes-internal
writePhenotypes.internal	phenotypes2genotypes-internal
writeSingleFile	phenotypes2genotypes-internal
