analyzeHaploClusters	analyzeHaploClusters
bicluster_id	HaploCluster-class
bicluster_id,HaploCluster-method	HaploCluster-class
bicluster_id<-	HaploCluster-class
bicluster_id<-,HaploCluster,numeric-method	HaploCluster-class
chr1ASW1000G	chr1ASW1000G
chromosome	HaploCluster-class
chromosome,HaploCluster-method	HaploCluster-class
chromosome<-	HaploCluster-class
chromosome<-,HaploCluster,character-method	HaploCluster-class
compareHaploClusterLists	compareHaploClusterLists
compareHaploClusterLists,HaploClusterList,ANY,character,ANY,ANY,numeric,numeric-method	compareHaploClusterLists
compareHaploClusterLists,HaploClusterList-method	compareHaploClusterLists
coreClusterIndividuals	HaploCluster-class
coreClusterIndividuals,HaploCluster-method	HaploCluster-class
coreClusterIndividuals<-	HaploCluster-class
coreClusterIndividuals<-,HaploCluster,vector-method	HaploCluster-class
extractHaploClusters	extractHaploClusters
extractHaploClusters,Factorization,list,data.frame,character,matrix,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric-method	extractHaploClusters
extractHaploClusters,Factorization-method	extractHaploClusters
findDenseRegions	findDenseRegions
hapFabia	hapFabia
hapFabiaVersion	hapFabiaVersion
HaploCluster	HaploCluster-class
HaploCluster,ANY-method	HaploCluster-class
HaploCluster,HaploCluster-method	HaploCluster-class
HaploCluster,numeric,numeric,character,numeric,numeric,numeric,numeric,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector-method	HaploCluster-class
HaploCluster-class	HaploCluster-class
HaploCluster-method	HaploCluster-class
haploClusterLength	HaploCluster-class
haploClusterLength,HaploCluster-method	HaploCluster-class
haploClusterLength<-	HaploCluster-class
haploClusterLength<-,HaploCluster,numeric-method	HaploCluster-class
HaploClusterList	HaploClusterList-class
HaploClusterList,ANY-method	HaploClusterList-class
HaploClusterList,list,numeric,list-method	HaploClusterList-class
HaploClusterList-class	HaploClusterList-class
HaploClusterList-method	HaploClusterList-class
haploClusterList2excel	haploClusterList2excel
haploClusterList2excel,HaploClusterList,character-method	haploClusterList2excel
haploClusterList2excel,HaploClusterList-method	haploClusterList2excel
haploClusterPos	HaploCluster-class
haploClusterPos,HaploCluster-method	HaploCluster-class
haploClusterPos<-	HaploCluster-class
haploClusterPos<-,HaploCluster,numeric-method	HaploCluster-class
haploClusters	HaploClusterList-class
haploClusters,HaploClusterList-method	HaploClusterList-class
haploClusters<-	HaploClusterList-class
haploClusters<-,HaploClusterList,list-method	HaploClusterList-class
hapRes	hapRes
histL	toolsFactorizationClass
histL,Factorization,numeric,ANY,ANY,numeric,numeric-method	toolsFactorizationClass
histL,Factorization-method	toolsFactorizationClass
ID	HaploCluster-class
ID,HaploCluster-method	HaploCluster-class
ID<-	HaploCluster-class
ID<-,HaploCluster,numeric-method	HaploCluster-class
identifyDuplicates	identifyDuplicates
idIndividuals	HaploCluster-class
idIndividuals,HaploCluster-method	HaploCluster-class
idIndividuals<-	HaploCluster-class
idIndividuals<-,HaploCluster,vector-method	HaploCluster-class
individualPerTagSNV	HaploCluster-class
individualPerTagSNV,HaploCluster-method	HaploCluster-class
individualPerTagSNV<-	HaploCluster-class
individualPerTagSNV<-,HaploCluster,vector-method	HaploCluster-class
individuals	HaploCluster-class
individuals,HaploCluster-method	HaploCluster-class
individuals<-	HaploCluster-class
individuals<-,HaploCluster,vector-method	HaploCluster-class
iterateSegments	iterateSegments
labelIndividuals	HaploCluster-class
labelIndividuals,HaploCluster-method	HaploCluster-class
labelIndividuals<-	HaploCluster-class
labelIndividuals<-,HaploCluster,vector-method	HaploCluster-class
lengthList	HaploClusterList-class
lengthList,HaploClusterList-method	HaploClusterList-class
lengthList<-	HaploClusterList-class
lengthList<-,HaploClusterList,numeric-method	HaploClusterList-class
makePipelineFile	makePipelineFile
matrixPlot	matrixPlot
mergedHaploClusterList	mergedHaploClusterList
mergeHaploClusterLists	mergeHaploClusterLists
mergeHaploClusterLists,HaploClusterList,ANY,vector-method	mergeHaploClusterLists
mergeHaploClusterLists,HaploClusterList-method	mergeHaploClusterLists
numberIndividuals	HaploCluster-class
numberIndividuals,HaploCluster-method	HaploCluster-class
numberIndividuals<-	HaploCluster-class
numberIndividuals<-,HaploCluster,numeric-method	HaploCluster-class
numbertagSNVs	HaploCluster-class
numbertagSNVs,HaploCluster-method	HaploCluster-class
numbertagSNVs<-	HaploCluster-class
numbertagSNVs<-,HaploCluster,numeric-method	HaploCluster-class
platformIndividuals	HaploCluster-class
platformIndividuals,HaploCluster-method	HaploCluster-class
platformIndividuals<-	HaploCluster-class
platformIndividuals<-,HaploCluster,vector-method	HaploCluster-class
plot,HaploCluster,missing-method	HaploCluster-class
plot,HaploCluster-method	HaploCluster-class
plot,HaploClusterList,missing-method	HaploClusterList-class
plot,HaploClusterList-method	HaploClusterList-class
plotHaplotypeCluster	plotHaplotypeCluster
plotL	toolsFactorizationClass
plotL,Factorization,numeric,ANY,ANY,character,numeric,numeric,character,numeric-method	toolsFactorizationClass
plotL,Factorization-method	toolsFactorizationClass
populationIndividuals	HaploCluster-class
populationIndividuals,HaploCluster-method	HaploCluster-class
populationIndividuals<-	HaploCluster-class
populationIndividuals<-,HaploCluster,vector-method	HaploCluster-class
res	res
setAnnotation	setAnnotation
setAnnotation,HaploClusterList,character-method	setAnnotation
setAnnotation,HaploClusterList-method	setAnnotation
setStatistics	setStatistics
setStatistics,HaploClusterList-method	setStatistics
sim	sim
simu	simu
simulateHaploClustersFabia	simulateHaploClustersFabia
simulateHaplotypeClusters	simulateHaplotypeClusters
split_sparse_matrix	split_sparse_matrix
statistics	HaploClusterList-class
statistics,HaploClusterList-method	HaploClusterList-class
statistics<-	HaploClusterList-class
statistics<-,HaploClusterList,list-method	HaploClusterList-class
summary,HaploCluster-method	HaploCluster-class
summary,HaploClusterList-method	HaploClusterList-class
tagSNVAlleles	HaploCluster-class
tagSNVAlleles,HaploCluster-method	HaploCluster-class
tagSNVAlleles<-	HaploCluster-class
tagSNVAlleles<-,HaploCluster,vector-method	HaploCluster-class
tagSNVAnno	HaploCluster-class
tagSNVAnno,HaploCluster-method	HaploCluster-class
tagSNVAnno<-	HaploCluster-class
tagSNVAnno<-,HaploCluster,vector-method	HaploCluster-class
tagSNVChange	HaploCluster-class
tagSNVChange,HaploCluster-method	HaploCluster-class
tagSNVChange<-	HaploCluster-class
tagSNVChange<-,HaploCluster,vector-method	HaploCluster-class
tagSNVFreq	HaploCluster-class
tagSNVFreq,HaploCluster-method	HaploCluster-class
tagSNVFreq<-	HaploCluster-class
tagSNVFreq<-,HaploCluster,vector-method	HaploCluster-class
tagSNVGroupFreq	HaploCluster-class
tagSNVGroupFreq,HaploCluster-method	HaploCluster-class
tagSNVGroupFreq<-	HaploCluster-class
tagSNVGroupFreq<-,HaploCluster,vector-method	HaploCluster-class
tagSNVNames	HaploCluster-class
tagSNVNames,HaploCluster-method	HaploCluster-class
tagSNVNames<-	HaploCluster-class
tagSNVNames<-,HaploCluster,vector-method	HaploCluster-class
tagSNVPositions	HaploCluster-class
tagSNVPositions,HaploCluster-method	HaploCluster-class
tagSNVPositions<-	HaploCluster-class
tagSNVPositions<-,HaploCluster,vector-method	HaploCluster-class
tagSNVs	HaploCluster-class
tagSNVs,HaploCluster-method	HaploCluster-class
tagSNVs<-	HaploCluster-class
tagSNVs<-,HaploCluster,vector-method	HaploCluster-class
tagSNVsPerIndividual	HaploCluster-class
tagSNVsPerIndividual,HaploCluster-method	HaploCluster-class
tagSNVsPerIndividual<-	HaploCluster-class
tagSNVsPerIndividual<-,HaploCluster,vector-method	HaploCluster-class
toolsFactorizationClass	toolsFactorizationClass
topLZ	toolsFactorizationClass
topLZ,Factorization,numeric,character,logical,ANY,ANY-method	toolsFactorizationClass
topLZ,Factorization,numeric,character,logical,ANY-method	toolsFactorizationClass
topLZ,Factorization,numeric,character,logical-method	toolsFactorizationClass
topLZ,Factorization-method	toolsFactorizationClass
vcftoFABIA	vcftoFABIA
[	HaploClusterList-class
[,HaploClusterList,numeric,missing-method	HaploClusterList-class
[,HaploClusterList-method	HaploClusterList-class
[<-	HaploClusterList-class
[<-,HaploClusterList,numeric,missing,HaploClusterList-method	HaploClusterList-class
[<-,HaploClusterList-method	HaploClusterList-class
[[	HaploClusterList-class
[[,HaploClusterList,numeric,missing-method	HaploClusterList-class
[[,HaploClusterList-method	HaploClusterList-class
[[<-	HaploClusterList-class
[[<-,HaploClusterList,numeric,missing,HaploCluster-method	HaploClusterList-class
[[<-,HaploClusterList-method	HaploClusterList-class
