MinimumDistance-package	MinimumDistance
"[",ff_array,ANY-method	TrioSet-class
"[",Pedigree,ANY-method	Pedigree-class
"[",TrioSet,ANY-method	TrioSet-class
"[",TrioSetList,ANY-method	TrioSetList-class
"[[",ParentOffspringList,ANY,ANY-method	ParentOffspringList-class
"[[",TrioSetList,ANY,ANY-method	TrioSetList-class
$,TrioSetList-method	TrioSetList-class
acf2	acf2
calculateMindist	calculateMindist
calculateMindist,arrayORff_array-method	calculateMindist
calculateMindist,list-method	calculateMindist
calculateMindist,matrix-method	calculateMindist
calculateMindist,TrioSet-method	calculateMindist
calculateMindist,TrioSetList-method	calculateMindist
coerce	coercion-methods
coerce,RangedDataCNV,GRanges-class	Defunct
coerce,TrioSet,data.frame-method	coercion-methods
coerce,TrioSet,TrioSetList-method	coercion-methods
coerce,TrioSetList,RangedSummarizedExperiment-method	TrioSetList-class
Defunct	Defunct
denovo	denovo
denovo,MinDistPosterior-method	denovo
denovoDuplication	denovo
denovoDuplication,MinDistPosterior-method	denovo
denovoHemizygous	denovo
denovoHemizygous,MinDistPosterior-method	denovo
denovoHomozygous	denovo
denovoHomozygous,MinDistPosterior-method	denovo
dim,Pedigree-method	Pedigree-class
dim,TrioSet-method	TrioSet-class
DNAcopyParam	DNAcopyParam
exampleTrioSetList	exampleTrioSetList
father	ParentOffspring-class
father,MinDistExperiment-method	MinDistExperiment-class
father,MinDistGRanges-method	MinDistGRanges-class
father,ParentOffspring-method	ParentOffspring-class
father,RangedSummarizedExperiment-method	MinDistExperiment-class
filterExperiment	filterExperiment
filterExperiment,MinDistExperiment,GRanges-method	filterExperiment
filterExperiment,MinDistExperiment,GRangesList-method	filterExperiment
filterExperiment,MinDistExperiment,MinDistGRanges-method	filterExperiment
FilterParamMD	FilterParamMD
FilterParamMD-class	FilterParamMD-class
length,ParentOffspringList-method	ParentOffspringList-class
length,TrioSetList-method	TrioSetList-class
mad2	mad2
mad2,array-method	mad2
mad2,list-method	mad2
mad2,matrix-method	mad2
mad2,TrioSetList-method	mad2
MAP	MAP
MAP,TrioSet,GRanges-method	TrioSet-class
MAP,TrioSetList,GRanges-method	TrioSetList-class
MAP2	MAP2
MAP2,MinDistExperiment,GRanges-method	MAP2
MAP2,MinDistExperiment,GRangesList-method	MAP2
MAP2,MinDistExperiment,MinDistGRanges-method	MAP2
mdLegend	mdLegend
MDRanges	MDRanges-class
MDRanges-class	MDRanges-class
md_exp	md_exp
md_gr	md_gr
mindist	mindist
mindist,MinDistExperiment-method	MinDistExperiment-class
mindist,MinDistGRanges-method	MinDistGRanges-class
mindist,TrioSet-method	TrioSet-class
mindist<-	mindist
mindist<-,MinDistExperiment,ANY-method	MinDistExperiment-class
mindist<-,MinDistGRanges,GRangesList-method	MinDistGRanges-class
mindist<-,TrioSet,matrix-method	TrioSet-class
MinDistExperiment	MinDistExperiment
MinDistExperiment,ArrayViews,ParentOffspring-method	MinDistExperiment
MinDistExperiment-class	MinDistExperiment-class
MinDistGRanges	MinDistGRanges
MinDistGRanges-class	MinDistGRanges-class
MinDistParam	MinDistParam
MinDistParam-class	MinDistParam-class
MinDistPosterior-class	MinDistPosterior-class
MinimumDistance	MinimumDistance
mother	ParentOffspring-class
mother,MinDistExperiment-method	MinDistExperiment-class
mother,MinDistGRanges-method	MinDistGRanges-class
mother,ParentOffspring-method	ParentOffspring-class
mother,RangedSummarizedExperiment-method	MinDistExperiment-class
names,MinDistGRanges-method	MinDistGRanges-class
names,ParentOffspring-method	ParentOffspring-class
nMAD	nMAD
nMAD,MinDistParam-method	MinDistParam-class
nMAD<-	nMAD
nMAD<-,MinDistParam,numeric-method	MinDistParam-class
offspring	ParentOffspring-class
offspring,GRangesList-method	MinDistGRanges-class
offspring,MinDistExperiment-method	MinDistExperiment-class
offspring,MinDistGRanges-method	MinDistGRanges-class
offspring,ParentOffspring-method	ParentOffspring-class
offspring,RangedSummarizedExperiment-method	MinDistExperiment-class
offspringNames	Deprecated
offspringNames,Pedigree-method	Pedigree-class
offspringNames,TrioSetList-method	TrioSetList-class
offspringNames<-	Deprecated
ParentOffspring	ParentOffspring-class
ParentOffspring-class	ParentOffspring-class
ParentOffspringList	ParentOffspringList-class
ParentOffspringList-class	ParentOffspringList-class
Pedigree	Pedigree
pedigree	Deprecated
pedigree,MinDistExperiment-method	MinDistExperiment-class
pedigree,MinDistGRanges-method	MinDistGRanges-class
pedigree,TrioSet-method	TrioSet-class
pedigree,TrioSetList-method	TrioSetList-class
Pedigree-class	Pedigree-class
pedigree<-	Deprecated
pedigree<-,MinDistExperiment-method	MinDistExperiment-class
pedigreeGrid	pedigreeGrid
pedigreeName	pedigreeName
pedigreeName,ParentOffspring-method	ParentOffspring-class
pedigreeName,ParentOffspringList-method	ParentOffspringList-class
pedigreeViewports	pedigreeViewports
PennParam	PennParam
plotDenovo	plotDenovo
plotDenovo,MinDistExperiment,MDRanges-method	plotDenovo
range,ILimit-method	range-ILimit-method
segment2	segment2
segment2,arrayORff_array-method	segment2
segment2,ff_matrix-method	segment2
segment2,list-method	TrioSetList-class
segment2,matrix-method	segment2
segment2,MinDistExperiment-method	MinDistExperiment-class
segment2,TrioSet-method	segment2
segment2,TrioSetList-method	TrioSetList-class
show,DNAcopyParam-method	MinDistParam-class
show,FilterParamMD-method	FilterParamMD-class
show,MinDistExperiment-method	MinDistExperiment-class
show,MinDistGRanges-method	MinDistGRanges-class
show,MinDistParam-method	MinDistParam-class
show,MinDistPosterior-method	MinDistPosterior-class
show,ParentOffspring-method	ParentOffspring-class
show,ParentOffspringList-method	ParentOffspringList-class
show,Pedigree-method	Pedigree-class
show,PennParam-method	PennParam
show,TrioSet-method	TrioSet-class
show,TrioSetList-method	TrioSetList-class
stack,TrioSetLiset-method	coercion-methods
stack,TrioSetList-method	coercion-methods
trios	Deprecated
trios,Pedigree-method	Pedigree-class
trios,TrioSet-method	TrioSet-class
trios,TrioSetList-method	TrioSetList-class
TrioSet	TrioSet
TrioSet-class	TrioSet-class
TrioSetList	TrioSetList
trioSetList	exampleTrioSetList
TrioSetList-class	TrioSetList-class
TrioSetListLD	TrioSetListLD
[,ff_array,ANY,ANY,ANY-method	TrioSet-class
[,MinDistExperiment,ANY,ANY,ANY-method	MinDistExperiment-class
[,MinDistPosterior,ANY,ANY,ANY-method	MinDistPosterior-class
[,ParentOffspringList,ANY,ANY,ANY-method	ParentOffspringList-class
[,ParentOffspringList,ANY-method	ParentOffspringList-class
[,Pedigree,ANY,ANY,ANY-method	Pedigree-class
[,TrioSet,ANY,ANY,ANY-method	TrioSet-class
[,TrioSetList,ANY,ANY,ANY-method	TrioSetList-class
[[,ParentOffspringList,ANY,ANY-method	ParentOffspringList-class
[[,TrioSetList,ANY,ANY-method	TrioSetList-class
