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
