$,TrioSetList-method	TrioSetList-class
allNames	TrioSetList-class
allNames,Pedigree-method	Pedigree-class
allNames,TrioSet-method	TrioSet-class
allNames,TrioSetList-method	TrioSetList-class
annotatedDataFrameFrom,array,ANY-method	annotatedDataFrameFrom-methods
annotatedDataFrameFrom,ff_array,ANY-method	annotatedDataFrameFrom-methods
annotatedDataFrameFrom,ff_matrix,ANY-method	annotatedDataFrameFrom-methods
annotatedDataFrameFrom,matrix,ANY-method	annotatedDataFrameFrom-methods
annotatedDataFrameFrom,Pedigree,logical-method	annotatedDataFrameFrom-methods
annotatedDataFrameFrom-methods	annotatedDataFrameFrom-methods
annotation,TrioSetList-method	TrioSetList-class
baf	TrioSetList-class
baf,TrioSet-method	TrioSet-class
baf,TrioSetList-method	TrioSetList-class
baf<-	TrioSet-class
baf<-,TrioSet,array-method	TrioSet-class
baf<-,TrioSet,ff_array-method	TrioSet-class
baf<-,TrioSet-method	TrioSet-class
calculateMindist	calculateMindist
calculateMindist,arrayORff_array-method	calculateMindist
calculateMindist,list-method	calculateMindist
calculateMindist,TrioSet-method	TrioSet-class
calculateMindist,TrioSetList-method	calculateMindist
callDenovoSegments	callDenovoSegments
coerce,RangedDataCNV,GRanges-method	coerce-methods
coerce,TrioSet,data.frame-method	TrioSet-class
coerce,TrioSet,TrioSetList-method	TrioSet-class
computeBayesFactor	computeBayesFactor
computeBayesFactor,TrioSet-method	TrioSet-class
computeBayesFactor,TrioSetList-method	TrioSetList-class
concAtTop	concordance
correspondingCall	correspondingCall
dim,Pedigree-method	Pedigree-class
dim,TrioSet-method	TrioSet-class
dims,TrioSetList-method	TrioSetList-class
discAtTop	concordance
fatherNames	TrioSetList-class
fatherNames,Pedigree-method	Pedigree-class
fatherNames,TrioSet-method	TrioSet-class
fatherNames,TrioSetList-method	TrioSetList-class
fatherNames<-	TrioSet-class
fatherNames<-,TrioSet,character-method	TrioSet-class
fatherPhenoData	phenoData
fatherPhenoData,TrioSet-method	TrioSet-class
fatherPhenoData,TrioSetList-method	TrioSetList-class
featureData,TrioSetList-method	TrioSetList-class
gcSubtract	gcSubtract
gcSubtract,TrioSet-method	TrioSet-class
gcSubtract,TrioSetList-method	TrioSetList-class
initialize,Pedigree-method	Pedigree-class
initialize,TrioSet-method	TrioSet-class
initialize,TrioSetList-method	TrioSetList-class
isDenovo	isDenovo
length,TrioSetList-method	TrioSetList-class
lrr,TrioSet-method	TrioSet-class
lrr,TrioSetList-method	TrioSetList-class
lrr.segs	lrr.segs
lrr<-	TrioSet-class
lrr<-,TrioSet-method	TrioSet-class
mad2	mad2
mad2,array-method	mad2
mad2,list-method	mad2
mad2,matrix-method	mad2
mad2,TrioSetList-method	TrioSetList-class
map.segs	lrr.segs
md.segs	lrr.segs
mindist	TrioSet-class
mindist,TrioSet-method	TrioSet-class
mindist,TrioSetList-method	TrioSetList-class
mindist<-	TrioSet-class
mindist<-,TrioSet,matrix-method	TrioSet-class
mindist<-,TrioSetList,list-method	TrioSetList-class
motherNames	TrioSetList-class
motherNames,Pedigree-method	Pedigree-class
motherNames,TrioSet-method	TrioSet-class
motherNames,TrioSetList-method	TrioSetList-class
motherPhenoData	phenoData
motherPhenoData,TrioSet-method	TrioSet-class
motherPhenoData,TrioSetList-method	TrioSetList-class
narrow	narrow
ncol,TrioSet-method	TrioSet-class
ncol,TrioSetList-method	TrioSetList-class
nrow,TrioSetList-method	TrioSetList-class
offspringNames	TrioSetList-class
offspringNames,Pedigree-method	Pedigree-class
offspringNames,TrioSet-method	TrioSet-class
offspringNames,TrioSetList-method	TrioSetList-class
offspringPhenoData	TrioSet-class
offspringPhenoData,TrioSet-method	TrioSet-class
offspringPhenoData,TrioSetList-method	TrioSetList-class
order,TrioSet-method	TrioSet-class
order,TrioSetList-method	TrioSetList-class
Pedigree	Pedigree
pedigree	TrioSetList-class
pedigree,TrioSet-method	TrioSet-class
pedigree,TrioSetList-method	TrioSetList-class
Pedigree-class	Pedigree-class
phenoData,TrioSetList-method	TrioSetList-class
sampleNames,TrioSetList-method	TrioSetList-class
segment2	segment2
segment2,arrayORff_array-method	segment2
segment2,ff_matrix-method	segment2
segment2,list-method	segment2
segment2,matrix-method	segment2
segment2,TrioSet-method	segment2
segment2,TrioSetList-method	segment2
stack,TrioSetList-method	TrioSetList-class
stackRangedDataList	stackRangedDataList
trios	TrioSetList-class
trios,Pedigree-method	Pedigree-class
trios,TrioSet-method	TrioSet-class
trios,TrioSetList-method	TrioSetList-class
TrioSet	TrioSet
TrioSet-class	TrioSet-class
TrioSetList	trioSetList
trioSetList	trioSetListExample
TrioSetList-class	TrioSetList-class
trioSetListExample	trioSetListExample
TrioSetListLD	TrioSetListLD
updateObject,TrioSet-method	TrioSet-class
updateObject,TrioSetList-method	TrioSetList-class
xypanelTrio	xypanelTrio
xyplot,formula,TrioSet-method	TrioSet-class
xyplotTrio	xyplotTrio
xyplotTrioLrrBaf	defunct
[,ff_array-method	TrioSet-class
[,Pedigree-method	Pedigree-class
[,TrioSet-method	TrioSet-class
[,TrioSetList-method	TrioSetList-class
[[,TrioSetList,ANY,ANY-method	TrioSetList-class
