Reference

All functions
AND()	AND
OR()	OR
TCGA.map.clinical.data()	TCGA.map.clinical.data
TCGA.multiple.samples()	TCGA.multiple.samples
TCGA.remove.multiple.samples()	TCGA.remove.multiple.samples
TCGA.shorten.barcodes()	TCGA.shorten.barcodes
XOR()	XOR
aCML	Atypical chronic myeloid leukemia dataset
annotate.description()	annotate.description
annotate.stages()	annotate.stages
as.adj.matrix()	as.adj.matrix
as.alterations()	as.alterations
as.bootstrap.scores()	as.bootstrap.scores
as.colors()	as.colors
as.conditional.probs()	as.conditional.probs
as.confidence()	as.confidence
as.description()	as.description
as.events()	as.events
as.events.in.patterns()	as.events.in.patterns
as.events.in.sample()	as.events.in.sample
as.gene()	as.gene
as.genes()	as.genes
as.genes.in.patterns()	as.genes.in.patterns
as.genotypes()	as.genotypes
as.hypotheses()	as.hypotheses
as.joint.probs()	as.joint.probs
as.kfold.eloss()	as.kfold.eloss
as.kfold.posterr()	as.kfold.posterr
as.kfold.prederr()	as.kfold.prederr
as.marginal.probs()	as.marginal.probs
as.models()	as.models
as.parameters()	as.parameters
as.pathway()	as.pathway
as.patterns()	as.patterns
as.samples()	as.samples
as.selective.advantage.relations()	as.selective.advantage.relations
as.stages()	as.stages
as.types()	as.types
as.types.in.patterns()	as.types.in.patterns
change.color()	change.color
consolidate.data()	consolidate.data
crc_gistic	GISTIC example data
crc_maf	MAF example data
crc_plain	Plain mutation dataset
delete.event()	delete.event
delete.gene()	delete.gene
delete.hypothesis()	delete.hypothesis
delete.model()	delete.model
delete.pattern()	delete.pattern
delete.samples()	delete.samples
delete.type()	delete.type
duplicates()	duplicates
ebind()	ebind
enforce.numeric()	enforce.numeric
enforce.string()	enforce.string
events.selection()	events.selection
export.graphml()	export.graphml
export.mutex()	export,mutex
export.nbs.input()	export.nbs.input
extract.MAF.HuGO.Entrez.map()	extract.MAF.HuGO.Entrez.map
genes.table.report()	genes.table.report
has.duplicates()	has.duplicates
has.model()	has.model
has.stages()	has stages
hypothesis.add()	hypothesis add
hypothesis.add.group()	hypothesis add group
hypothesis.add.homologous()	hypothesis.add.homologous
import.GISTIC()	import.GISTIC
import.MAF()	import.MAF
import.genotypes()	import.genotypes
import.model()	import.model
import.mutex.groups()	import.mutex.groups
intersect.datasets()	intersect.datasets
is.compliant()	is.compliant
join.events()	join.events
join.types()	join.types
keysToNames()	keysToNames
maf	MAF example data
muts	Simple mutation dataset
nameToKey()	nameToKey
nevents()	nevents
ngenes()	ngenes
nhypotheses()	Return the number of hypotheses in the dataset
npatterns()	Return the number of patterns in the dataset
nsamples()	nsamples
ntypes()	ntypes
oncoprint()	oncoprint
oncoprint.cbio()	oncoprint.cbio
order.frequency()	order.frequency
pathway.visualization()	pathway.visualization
pheatmap()	A function to draw clustered heatmaps.
rank.recurrents()	rank.recurrents
rename.gene()	rename.gene
rename.type()	rename.type
samples.selection()	samples.selection
sbind()	sbind
ssplit()	ssplit
stage	Stage information for test_dataset
test_dataset	A complete dataset with hypotheses
test_dataset_no_hypos	A complete dataset
test_model	A complete dataset with a reconstructed model
test_model_kfold	A complete dataset with a reconstructed model and crossvalidation informations
trim()	trim
tronco.bootstrap()	tronco bootstrap
tronco.caprese()	tronco caprese
tronco.capri()	tronco capri
tronco.chowliu()	Tronco Chow Liu
tronco.edmonds()	Tronco Edmonds
tronco.gabow()	Tronco Gabow
tronco.kfold.eloss()	tronco.kfold.eloss
tronco.kfold.posterr()	tronco.kfold.posterr. For details and examples regarding the statistical assesment of an inferred model, we refer to the Vignette Section 7.
tronco.kfold.prederr()	tronco.kfold.prederr
tronco.pattern.plot()	tronco.pattern.plot
tronco.plot()	tronco.plot
tronco.prim()	Tronco Prim
view()	view
which.samples()	which.samples