# TRONCO, an R package for TRanslational ONCOlogy

## Documentation for package ‘TRONCO’ version 2.10.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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 --

cbio.query | cbio.query
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