TRONCO, an R package for TRanslational ONCOlogy

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Documentation for package ‘TRONCO’ version 2.41.0

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A C D E G H I J K M N O P R S T V W X

-- A --

aCML Atypical chronic myeloid leukemia dataset
AND AND
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

-- C --

change.color change.color
consolidate.data consolidate.data
crc_gistic GISTIC example data
crc_maf MAF example data
crc_plain Plain mutation dataset

-- D --

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

-- E --

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

-- G --

genes.table.report genes.table.report

-- H --

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

-- I --

import.genotypes import.genotypes
import.GISTIC import.GISTIC
import.MAF import.MAF
import.model import.model
import.mutex.groups import.mutex.groups
intersect.datasets intersect.datasets
is.compliant is.compliant

-- J --

join.events join.events
join.types join.types

-- K --

keysToNames keysToNames

-- M --

maf MAF example data
muts Simple mutation dataset

-- N --

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

-- O --

oncoprint oncoprint
oncoprint.cbio oncoprint.cbio
OR OR
order.frequency order.frequency

-- P --

pathway.visualization pathway.visualization
pheatmap A function to draw clustered heatmaps.

-- R --

rank.recurrents rank.recurrents
rename.gene rename.gene
rename.type rename.type

-- S --

samples.selection samples.selection
sbind sbind
ssplit ssplit
stage Stage information for test_dataset

-- T --

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
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

-- V --

view view

-- W --

which.samples which.samples

-- X --

XOR XOR