HEMDAG-package	HEMDAG-package
ancestors	ancestors
AUPRC.single.class	AUPRC.single.class
AUPRC.single.over.classes	AUPRC.single.over.classes
AUROC.single.class	AUROC.single.class
AUROC.single.over.classes	AUROC.single.over.classes
build.ancestors	ancestors
build.ancestors.bottom.up	ancestors
build.ancestors.per.level	ancestors
build.children	children
build.descendants	descendants
build.descendants.bottom.up	descendants
build.descendants.per.level	descendants
check.annotation.matrix.integrity	check.annotation.matrix.integrity
check.DAG.integrity	check.DAG.integrity
check.hierarchy	hierarchical.checkers
check.hierarchy.single.sample	hierarchical.checkers
children	children
compute.flipped.graph	compute.flipped.graph
constraints.matrix	constraints.matrix
descendants	descendants
DESCENS	DESCENS
descens.tau	DESCENS
descens.threshold	DESCENS
descens.threshold.free	DESCENS
descens.weighted.threshold	DESCENS
descens.weighted.threshold.free	DESCENS
distances.from.leaves	distances.from.leaves
do.edges.from.HPO.obo	do.edges.from.HPO.obo
Do.FLAT.scores.normalization	Do.FLAT.scores.normalization
Do.full.annotation.matrix	Do.full.annotation.matrix
Do.heuristic.methods	Do.heuristic.methods
Do.heuristic.methods.holdout	Do.heuristic.methods.holdout
Do.HTD	Do.HTD
Do.HTD.holdout	Do.HTD.holdout
do.stratified.cv.data.over.classes	stratified.cross.validation
do.stratified.cv.data.single.class	stratified.cross.validation
do.subgraph	do.subgraph
do.submatrix	do.submatrix
Do.TPR.DAG	TPR-DAG-cross-validation
Do.TPR.DAG.holdout	TPR-DAG-holdout
do.unstratified.cv.data	do.unstratified.cv.data
example.datasets	example.datasets
F.measure.multilabel	Multilabel.F.measure
F.measure.multilabel,matrix,matrix-method	Multilabel.F.measure
find.best.f	find.best.f
find.leaves	find.leaves
full.annotation.matrix	full.annotation.matrix
g	example.datasets
get.children.bottom.up	children
get.children.top.down	children
get.parents	parents
get.parents.bottom.up	parents
get.parents.top.down	parents
get.parents.topological.sorting	parents
graph.levels	graph.levels
HEMDAG	HEMDAG-package
Heuristic-Methods	Heuristic-Methods
heuristicAND	Heuristic-Methods
heuristicMAX	Heuristic-Methods
heuristicOR	Heuristic-Methods
hierarchical.checkers	hierarchical.checkers
htd	HTD-DAG
HTD-DAG	HTD-DAG
L	example.datasets
Multilabel.F.measure	Multilabel.F.measure
normalize.max	normalize.max
parents	parents
read.graph	read.graph
read.undirected.graph	read.undirected.graph
root.node	root.node
S	example.datasets
specific.annotation.list	specific.annotation.list
specific.annotation.matrix	specific.annotation.matrix
stratified.cross.validation	stratified.cross.validation
test.index	example.datasets
TPR-DAG	TPR-DAG
TPR-DAG-cross-validation	TPR-DAG-cross-validation
TPR-DAG-holdout	TPR-DAG-holdout
TPR-DAG-variants	TPR-DAG-variants
TPR.DAG	TPR-DAG-variants
tpr.threshold	TPR-DAG
tpr.threshold.free	TPR-DAG
tpr.weighted.threshold	TPR-DAG
tpr.weighted.threshold.free	TPR-DAG
transitive.closure.annotations	transitive.closure.annotations
tupla.matrix	tupla.matrix
W	example.datasets
weighted.adjacency.matrix	weighted.adjacency.matrix
write.graph	write.graph
