analyzeIBDsegments	analyzeIBDsegments
bicluster_id	IBDsegment-class
bicluster_id,IBDsegment-method	IBDsegment-class
bicluster_id<-	IBDsegment-class
bicluster_id<-,IBDsegment,numeric-method	IBDsegment-class
chr1ASW1000G	chr1ASW1000G
chromosome	IBDsegment-class
chromosome,IBDsegment-method	IBDsegment-class
chromosome<-	IBDsegment-class
chromosome<-,IBDsegment,character-method	IBDsegment-class
compareIBDsegmentLists	compareIBDsegmentLists
compareIBDsegmentLists,IBDsegmentList,ANY,character,ANY,ANY,numeric,numeric-method	compareIBDsegmentLists
compareIBDsegmentLists,IBDsegmentList-method	compareIBDsegmentLists
coreClusterIndividuals	IBDsegment-class
coreClusterIndividuals,IBDsegment-method	IBDsegment-class
coreClusterIndividuals<-	IBDsegment-class
coreClusterIndividuals<-,IBDsegment,vector-method	IBDsegment-class
extractIBDsegments	extractIBDsegments
extractIBDsegments,Factorization,list,data.frame,character,matrix,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric-method	extractIBDsegments
extractIBDsegments,Factorization-method	extractIBDsegments
findDenseRegions	findDenseRegions
hapFabia	hapFabia
hapFabiaVersion	hapFabiaVersion
hapRes	hapRes
histL	toolsFactorizationClass
histL,Factorization,numeric,ANY,ANY,numeric,numeric-method	toolsFactorizationClass
histL,Factorization-method	toolsFactorizationClass
IBDsegment	IBDsegment-class
IBDsegment,ANY-method	IBDsegment-class
IBDsegment,IBDsegment-method	IBDsegment-class
IBDsegment,numeric,numeric,character,numeric,numeric,numeric,numeric,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector-method	IBDsegment-class
IBDsegment-class	IBDsegment-class
IBDsegment-method	IBDsegment-class
IBDsegmentLength	IBDsegment-class
IBDsegmentLength,IBDsegment-method	IBDsegment-class
IBDsegmentLength<-	IBDsegment-class
IBDsegmentLength<-,IBDsegment,numeric-method	IBDsegment-class
IBDsegmentList	IBDsegmentList-class
IBDsegmentList,ANY-method	IBDsegmentList-class
IBDsegmentList,list,numeric,list-method	IBDsegmentList-class
IBDsegmentList-class	IBDsegmentList-class
IBDsegmentList-method	IBDsegmentList-class
IBDsegmentList2excel	IBDsegmentList2excel
IBDsegmentList2excel,IBDsegmentList,character-method	IBDsegmentList2excel
IBDsegmentList2excel,IBDsegmentList-method	IBDsegmentList2excel
IBDsegmentPos	IBDsegment-class
IBDsegmentPos,IBDsegment-method	IBDsegment-class
IBDsegmentPos<-	IBDsegment-class
IBDsegmentPos<-,IBDsegment,numeric-method	IBDsegment-class
IBDsegments	IBDsegmentList-class
IBDsegments,IBDsegmentList-method	IBDsegmentList-class
IBDsegments<-	IBDsegmentList-class
IBDsegments<-,IBDsegmentList,list-method	IBDsegmentList-class
ID	IBDsegment-class
ID,IBDsegment-method	IBDsegment-class
ID<-	IBDsegment-class
ID<-,IBDsegment,numeric-method	IBDsegment-class
identifyDuplicates	identifyDuplicates
idIndividuals	IBDsegment-class
idIndividuals,IBDsegment-method	IBDsegment-class
idIndividuals<-	IBDsegment-class
idIndividuals<-,IBDsegment,vector-method	IBDsegment-class
individualPerTagSNV	IBDsegment-class
individualPerTagSNV,IBDsegment-method	IBDsegment-class
individualPerTagSNV<-	IBDsegment-class
individualPerTagSNV<-,IBDsegment,vector-method	IBDsegment-class
individuals	IBDsegment-class
individuals,IBDsegment-method	IBDsegment-class
individuals<-	IBDsegment-class
individuals<-,IBDsegment,vector-method	IBDsegment-class
iterateIntervals	iterateIntervals
labelIndividuals	IBDsegment-class
labelIndividuals,IBDsegment-method	IBDsegment-class
labelIndividuals<-	IBDsegment-class
labelIndividuals<-,IBDsegment,vector-method	IBDsegment-class
lengthList	IBDsegmentList-class
lengthList,IBDsegmentList-method	IBDsegmentList-class
lengthList<-	IBDsegmentList-class
lengthList<-,IBDsegmentList,numeric-method	IBDsegmentList-class
makePipelineFile	makePipelineFile
matrixPlot	matrixPlot
mergedIBDsegmentList	mergedIBDsegmentList
mergeIBDsegmentLists	mergeIBDsegmentLists
mergeIBDsegmentLists,IBDsegmentList,ANY,vector-method	mergeIBDsegmentLists
mergeIBDsegmentLists,IBDsegmentList-method	mergeIBDsegmentLists
numberIndividuals	IBDsegment-class
numberIndividuals,IBDsegment-method	IBDsegment-class
numberIndividuals<-	IBDsegment-class
numberIndividuals<-,IBDsegment,numeric-method	IBDsegment-class
numbertagSNVs	IBDsegment-class
numbertagSNVs,IBDsegment-method	IBDsegment-class
numbertagSNVs<-	IBDsegment-class
numbertagSNVs<-,IBDsegment,numeric-method	IBDsegment-class
platformIndividuals	IBDsegment-class
platformIndividuals,IBDsegment-method	IBDsegment-class
platformIndividuals<-	IBDsegment-class
platformIndividuals<-,IBDsegment,vector-method	IBDsegment-class
plot,IBDsegment,missing-method	IBDsegment-class
plot,IBDsegment-method	IBDsegment-class
plot,IBDsegmentList,missing-method	IBDsegmentList-class
plot,IBDsegmentList-method	IBDsegmentList-class
plotIBDsegment	plotIBDsegment
plotL	toolsFactorizationClass
plotL,Factorization,numeric,ANY,ANY,character,numeric,numeric,character,numeric-method	toolsFactorizationClass
plotL,Factorization-method	toolsFactorizationClass
plotLarger	IBDsegment-class
plotLarger,IBDsegment,character,numeric-method	IBDsegment-class
plotLarger,IBDsegment,missing-method	IBDsegment-class
plotLarger,IBDsegment-method	IBDsegment-class
populationIndividuals	IBDsegment-class
populationIndividuals,IBDsegment-method	IBDsegment-class
populationIndividuals<-	IBDsegment-class
populationIndividuals<-,IBDsegment,vector-method	IBDsegment-class
res	res
setAnnotation	setAnnotation
setAnnotation,IBDsegmentList,character-method	setAnnotation
setAnnotation,IBDsegmentList-method	setAnnotation
setStatistics	setStatistics
setStatistics,IBDsegmentList-method	setStatistics
sim	sim
simu	simu
simulateIBDsegments	simulateIBDsegments
simulateIBDsegmentsFabia	simulateIBDsegmentsFabia
split_sparse_matrix	split_sparse_matrix
statistics	IBDsegmentList-class
statistics,IBDsegmentList-method	IBDsegmentList-class
statistics<-	IBDsegmentList-class
statistics<-,IBDsegmentList,list-method	IBDsegmentList-class
summary,IBDsegment-method	IBDsegment-class
summary,IBDsegmentList-method	IBDsegmentList-class
tagSNVAlleles	IBDsegment-class
tagSNVAlleles,IBDsegment-method	IBDsegment-class
tagSNVAlleles<-	IBDsegment-class
tagSNVAlleles<-,IBDsegment,vector-method	IBDsegment-class
tagSNVAnno	IBDsegment-class
tagSNVAnno,IBDsegment-method	IBDsegment-class
tagSNVAnno<-	IBDsegment-class
tagSNVAnno<-,IBDsegment,vector-method	IBDsegment-class
tagSNVChange	IBDsegment-class
tagSNVChange,IBDsegment-method	IBDsegment-class
tagSNVChange<-	IBDsegment-class
tagSNVChange<-,IBDsegment,vector-method	IBDsegment-class
tagSNVFreq	IBDsegment-class
tagSNVFreq,IBDsegment-method	IBDsegment-class
tagSNVFreq<-	IBDsegment-class
tagSNVFreq<-,IBDsegment,vector-method	IBDsegment-class
tagSNVGroupFreq	IBDsegment-class
tagSNVGroupFreq,IBDsegment-method	IBDsegment-class
tagSNVGroupFreq<-	IBDsegment-class
tagSNVGroupFreq<-,IBDsegment,vector-method	IBDsegment-class
tagSNVNames	IBDsegment-class
tagSNVNames,IBDsegment-method	IBDsegment-class
tagSNVNames<-	IBDsegment-class
tagSNVNames<-,IBDsegment,vector-method	IBDsegment-class
tagSNVPositions	IBDsegment-class
tagSNVPositions,IBDsegment-method	IBDsegment-class
tagSNVPositions<-	IBDsegment-class
tagSNVPositions<-,IBDsegment,vector-method	IBDsegment-class
tagSNVs	IBDsegment-class
tagSNVs,IBDsegment-method	IBDsegment-class
tagSNVs<-	IBDsegment-class
tagSNVs<-,IBDsegment,vector-method	IBDsegment-class
tagSNVsPerIndividual	IBDsegment-class
tagSNVsPerIndividual,IBDsegment-method	IBDsegment-class
tagSNVsPerIndividual<-	IBDsegment-class
tagSNVsPerIndividual<-,IBDsegment,vector-method	IBDsegment-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
[	IBDsegmentList-class
[,IBDsegmentList,numeric,missing-method	IBDsegmentList-class
[,IBDsegmentList-method	IBDsegmentList-class
[<-	IBDsegmentList-class
[<-,IBDsegmentList,numeric,missing,IBDsegmentList-method	IBDsegmentList-class
[<-,IBDsegmentList-method	IBDsegmentList-class
[[	IBDsegmentList-class
[[,IBDsegmentList,numeric,missing-method	IBDsegmentList-class
[[,IBDsegmentList-method	IBDsegmentList-class
[[<-	IBDsegmentList-class
[[<-,IBDsegmentList,numeric,missing,IBDsegment-method	IBDsegmentList-class
[[<-,IBDsegmentList-method	IBDsegmentList-class
