+,geneticData,assignFounderPattern-method	internalOperators
+,geneticData,assignFounderPatternPrototype-method	internalOperators
+,geneticData,biparentalDominant-method	internalOperators
+,geneticData,fixedNumberOfFounderAlleles-method	internalOperators
+,geneticData,multiparentSNP-method	internalOperators
+,geneticData,multiparentSNPPrototype-method	internalOperators
+,geneticData,normalPhenotype-method	internalOperators
+,mpcross,assignFounderPattern-method	internalOperators
+,mpcross,assignFounderPatternPrototype-method	internalOperators
+,mpcross,biparentalDominant-method	internalOperators
+,mpcross,fixedNumberOfFounderAlleles-method	internalOperators
+,mpcross,mpcross-method	combineMpcross
+,mpcross,multiparentSNP-method	internalOperators
+,mpcross,multiparentSNPPrototype-method	internalOperators
+,mpcross,normalPhenotype-method	internalOperators
+,mpcross,removeHets-method	internalOperators
+,mpcrossMapped,assignFounderPattern-method	internalOperators
+,mpcrossMapped,assignFounderPatternPrototype-method	internalOperators
+,mpcrossMapped,mpcrossMapped-method	combineMpcross
+,mpcrossRF,mpcross-method	combineMpcross
+,mpcrossRF,mpcrossRF-method	combineMpcross
.geneticData	geneticData-class
.mpcross	mpcross-class
.mpcrossMapped	mpcrossMapped-class
.mpcrossRF	mpcrossRF-class
.pedigreeGraph	pedigreeGraph-class
.probabilities	probabilities-class
addExtraMarkerFromRawCall	addExtraMarkerFromRawCall
addExtraMarkers	addExtraMarkers
as.mpInterval	as.mpInterval
assignFounderPattern	assignFounderPattern
backcrossPedigree	backcrossPedigree
biparentalDominant	biparentalDominant
callFromMap	callFromMap
changeMarkerPosition	changeMarkerPosition
clusterOrderCross	clusterOrderCross
combineKeepRF	combineKeepRF
computeAllEpistaticChiSquared	computeAllEpistaticChiSquared
computeGenotypeProbabilities	computeGenotypeProbabilities
detailedPedigree	detailedPedigree-class
detailedPedigree-class	detailedPedigree-class
eightParentPedigreeImproperFunnels	eightParentPedigreeImproperFunnels
eightParentPedigreeRandomFunnels	eightParentPedigreeRandomFunnels
eightParentPedigreeSingleFunnel	eightParentPedigreeSingleFunnel
eightParentSubsetMap	eightParentSubsetMap
estimateMap	estimateMap
estimateMapFromImputation	estimateMapFromImputation
estimateRF	estimateRF
estimateRFSingleDesign	estimateRFSingleDesign
existingLocalisationStatistics	existingLocalisationStatistics
expand	expand
exportMapToPretzl	exportMapToPretzl
extraImputationPoints	extraImputationPoints
f2Pedigree	f2Pedigree
finalNames	finalNames
finalNames,geneticData-method	finalNames
finalNames,mpcross-method	finalNames
finals	finals
finals,geneticData-method	finals
finals,mpcross-method	finals
fixedNumberOfFounderAlleles	fixedNumberOfFounderAlleles
flatImputationMapNames	flatImputationMapNames
flatImputationMapNames,geneticData-method	flatImputationMapNames
flatImputationMapNames,imputed-method	flatImputationMapNames
flatImputationMapNames,mpcrossMapped-method	flatImputationMapNames
formGroups	formGroups
founderNames	founderNames
founderNames,geneticData-method	founderNames
founderNames,mpcross-method	founderNames
founders	founders
founders,geneticData-method	founders
founders,mpcross-method	founders
fourParentPedigreeRandomFunnels	fourParentPedigreeRandomFunnels
fourParentPedigreeSingleFunnel	fourParentPedigreeSingleFunnel
fromMpMap	fromMpMap
generateGridPositions	generateGridPositions
generateIntervalMidPoints	generateIntervalMidPoints
geneticData-class	geneticData-class
getAllFunnels	getAllFunnels
getAllFunnelsIncAIC	getAllFunnelsIncAIC
getChromosomes	getChromosomes
getIntercrossingAndSelfingGenerations	getIntercrossingAndSelfingGenerations
getPositions	getPositions
haldane	mapFunctions
haldaneToRf	mapFunctions
hetData	hetData
hetData,geneticData-method	hetData
hetData,mpcross-method	hetData
hetsForSNPMarkers	hetsForSNPMarkers
imputationData	imputationData
imputationData,geneticData-method	imputationData
imputationData,imputed-method	imputationData
imputationData,mpcrossMapped-method	imputationData
imputationKey	imputationKey
imputationKey,geneticData-method	imputationKey
imputationKey,imputed-method	imputationKey
imputationKey,mpcrossMapped-method	imputationKey
imputationMap	imputationMap
imputationMap,geneticData-method	imputationMap
imputationMap,imputed-method	imputationMap
imputationMap,mpcrossMapped-method	imputationMap
impute	impute
imputeFounders	imputeFounders
infiniteSelfing	infiniteSelfing
initialize,canSkipValidity-method	initialize
initialize,geneticDataList-method	initialize
jitterMap	jitterMap
kosambi	mapFunctions
kosambiToRf	mapFunctions
lineNames	lineNamesGeneric
lineNames,geneticData-method	lineNamesMpcross
lineNames,mpcross-method	lineNamesMpcross
lineNames,pedigree-method	lineNamesPedigree
lineNames<-	lineNamesPedigree
lineNames<-,detailedPedigree-method	lineNamesPedigree
lineNames<-,pedigree-method	lineNamesPedigree
linesByNames	linesByNames
listCodingErrors	listCodingErrors
listCodingErrorsInfiniteSelfing	listCodingErrorsInfiniteSelfing
mapFunctions	mapFunctions
markers	markers
markers,geneticData-method	markers
markers,hetData-method	markers
markers,lg-method	markers
markers,mpcross-method	markers
markers,rf-method	markers
mpcross	mpcross
mpcross-class	mpcross-class
mpcrossMapped	mpcrossMapped
mpcrossMapped-class	mpcrossMapped-class
mpcrossRF-class	mpcrossRF-class
multiparentSNP	multiparentSNP
nFounders	nFounders
nFounders,detailedPedigree-method	nFounders
nFounders,geneticData-method	nFounders
nFounders,mpcross-method	nFounders
nFounders,pedigree-method	nFounders
nLines	nLines
nLines,geneticData-method	nLines
nLines,mpcross-method	nLines
nMarkers	nMarkers
nMarkers,geneticData-method	nMarkers
nMarkers,mpcross-method	nMarkers
normalPhenotype	normalPhenotype
omp_get_num_threads	openmp
omp_set_num_threads	openmp
orderCross	orderCross
pedigree	pedigree
pedigree-class	pedigree-class
pedigreeGraph-class	pedigreeGraph-class
pedigreeToGraph	pedigreeToGraph
plot,addExtraMarkersStatistics,ANY-method	plot-addExtraMarkersStatistics-ANY-method
plot,geneticData,ANY-method	plot
plot,imputed,ANY-method	plot
plot,mpcross,ANY-method	plot
plot,pedigreeGraph,ANY-method	plot-pedigreeGraph-ANY-method
plot,probabilities,ANY-method	plot
plotMosaic	plotMosaic
plotProbabilities	plotProbabilities
probabilities-class	probabilities-class
probabilityData	probabilityData
probabilityData,geneticData-method	probabilityData
probabilityData,mpcrossMapped-method	probabilityData
redact	redact
redact,geneticData-method	redact
redact,mpcross-method	redact
redact,mpcrossLG-method	redact
redact,mpcrossMapped-method	redact
redact,mpcrossRF-method	redact
removeHets	removeHets
reverseChromosomes	reverseChromosomes
rfToHaldane	mapFunctions
rfToKosambi	mapFunctions
rilPedigree	rilPedigree
selfing	selfing
selfing,pedigree-method	selfing
selfing<-	selfing
selfing<-,detailedPedigree-method	selfing
selfing<-,pedigree-method	selfing
simulatedFourParentData	simulatedFourParentData
simulatedFourParentMap	simulatedFourParentData
simulateMPCross	simulateMPCross
sixteenParentPedigreeRandomFunnels	sixteenParentPedigreeRandomFunnels
stripPedigree	stripPedigree
subset,geneticData-method	subset
subset,hetData-method	subset
subset,imputed-method	subset
subset,lg-method	subset
subset,mpcross-method	subset
subset,mpcrossLG-method	subset
subset,mpcrossMapped-method	subset
subset,mpcrossRF-method	subset
subset,probabilities-method	subset
subset,rawSymmetricMatrix-method	subset
subset,rf-method	subset
testDistortion	testDistortion
toMpMap	toMpMap
transposeProbabilities	transposeProbabilities
twoParentPedigree	twoParentPedigree
wsnp_Ku_rep_c103074_89904851	wsnp_Ku_rep_c103074_89904851
[,rawSymmetricMatrix,index,index,logical-method	internalOperators
[,rawSymmetricMatrix,index,index,missing-method	internalOperators
[,rawSymmetricMatrix,matrix,missing,missing-method	internalOperators
[,rawSymmetricMatrix,missing,missing,missing-method	internalOperators
