TRONCO: TRONCO, an R package for TRanslational ONCOlogy

The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference.

AuthorMarco Antoniotti [ctb], Giulio Caravagna [aut, cre], Luca De Sano [aut], Alex Graudenzi [aut], Giancarlo Mauri [ctb], Bud Mishra [ctb], Daniele Ramazzotti [aut]
Date of publicationNone
MaintainerBIMIB Group <tronco@disco.unimib.it>
Licensefile LICENSE
Version2.6.1
https://sites.google.com/site/troncopackage/

View on Bioconductor

Man pages

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

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

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.genotypes: import.genotypes

import.GISTIC: import.GISTIC

import.MAF: import.MAF

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

OR: OR

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

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...

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...

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

XOR: XOR

Files in this package

TRONCO/DESCRIPTION
TRONCO/LICENSE
TRONCO/NAMESPACE
TRONCO/R
TRONCO/R/as.functions.R TRONCO/R/bootstrap.R TRONCO/R/caprese.algorithm.R TRONCO/R/capri.algorithm.R TRONCO/R/capri.hypotheses.R TRONCO/R/chow.liu.algorithm.R TRONCO/R/correctness.R TRONCO/R/create.model.R TRONCO/R/data.R TRONCO/R/editing.functions.R TRONCO/R/edmonds.algorithm.R TRONCO/R/external.R TRONCO/R/gabow.algorithm.R TRONCO/R/loading.R TRONCO/R/lregfit.R TRONCO/R/prim.algorithm.R TRONCO/R/selection.R TRONCO/R/statistics.R TRONCO/R/tronco.R TRONCO/R/visualization.R TRONCO/R/which.functions.R
TRONCO/build
TRONCO/build/vignette.rds
TRONCO/data
TRONCO/data/aCML.RData
TRONCO/data/crc_gistic.RData
TRONCO/data/crc_maf.RData
TRONCO/data/crc_plain.RData
TRONCO/data/maf.csv
TRONCO/data/muts.RData
TRONCO/data/stage.RData
TRONCO/data/test_dataset.RData
TRONCO/data/test_dataset_no_hypos.RData
TRONCO/data/test_model.RData
TRONCO/data/test_model_kfold.RData
TRONCO/inst
TRONCO/inst/NEWS.Rd
TRONCO/inst/doc
TRONCO/inst/doc/vignette.R
TRONCO/inst/doc/vignette.Rnw
TRONCO/inst/doc/vignette.pdf
TRONCO/man
TRONCO/man/AND.Rd TRONCO/man/OR.Rd TRONCO/man/TCGA.map.clinical.data.Rd TRONCO/man/TCGA.multiple.samples.Rd TRONCO/man/TCGA.remove.multiple.samples.Rd TRONCO/man/TCGA.shorten.barcodes.Rd TRONCO/man/XOR.Rd TRONCO/man/aCML.Rd TRONCO/man/annotate.description.Rd TRONCO/man/annotate.stages.Rd TRONCO/man/as.adj.matrix.Rd TRONCO/man/as.alterations.Rd TRONCO/man/as.bootstrap.scores.Rd TRONCO/man/as.colors.Rd TRONCO/man/as.conditional.probs.Rd TRONCO/man/as.confidence.Rd TRONCO/man/as.description.Rd TRONCO/man/as.events.Rd TRONCO/man/as.events.in.patterns.Rd TRONCO/man/as.events.in.sample.Rd TRONCO/man/as.gene.Rd TRONCO/man/as.genes.Rd TRONCO/man/as.genes.in.patterns.Rd TRONCO/man/as.genotypes.Rd TRONCO/man/as.hypotheses.Rd TRONCO/man/as.joint.probs.Rd TRONCO/man/as.kfold.eloss.Rd TRONCO/man/as.kfold.posterr.Rd TRONCO/man/as.kfold.prederr.Rd TRONCO/man/as.marginal.probs.Rd TRONCO/man/as.models.Rd TRONCO/man/as.parameters.Rd TRONCO/man/as.pathway.Rd TRONCO/man/as.patterns.Rd TRONCO/man/as.samples.Rd TRONCO/man/as.selective.advantage.relations.Rd TRONCO/man/as.stages.Rd TRONCO/man/as.types.Rd TRONCO/man/as.types.in.patterns.Rd TRONCO/man/cbio.query.Rd TRONCO/man/change.color.Rd TRONCO/man/consolidate.data.Rd TRONCO/man/crc_gistic.Rd TRONCO/man/crc_maf.Rd TRONCO/man/crc_plain.Rd TRONCO/man/delete.event.Rd TRONCO/man/delete.gene.Rd TRONCO/man/delete.hypothesis.Rd TRONCO/man/delete.model.Rd TRONCO/man/delete.pattern.Rd TRONCO/man/delete.samples.Rd TRONCO/man/delete.type.Rd TRONCO/man/duplicates.Rd TRONCO/man/ebind.Rd TRONCO/man/enforce.numeric.Rd TRONCO/man/enforce.string.Rd TRONCO/man/events.selection.Rd TRONCO/man/export.graphml.Rd TRONCO/man/export.mutex.Rd TRONCO/man/export.nbs.input.Rd TRONCO/man/extract.MAF.HuGO.Entrez.map.Rd TRONCO/man/genes.table.report.Rd TRONCO/man/has.duplicates.Rd TRONCO/man/has.model.Rd TRONCO/man/has.stages.Rd TRONCO/man/hypothesis.add.Rd TRONCO/man/hypothesis.add.group.Rd TRONCO/man/hypothesis.add.homologous.Rd TRONCO/man/import.GISTIC.Rd TRONCO/man/import.MAF.Rd TRONCO/man/import.genotypes.Rd TRONCO/man/import.mutex.groups.Rd TRONCO/man/intersect.datasets.Rd TRONCO/man/is.compliant.Rd TRONCO/man/join.events.Rd TRONCO/man/join.types.Rd TRONCO/man/keysToNames.Rd TRONCO/man/maf.Rd TRONCO/man/muts.Rd TRONCO/man/nameToKey.Rd TRONCO/man/nevents.Rd TRONCO/man/ngenes.Rd TRONCO/man/nhypotheses.Rd TRONCO/man/npatterns.Rd TRONCO/man/nsamples.Rd TRONCO/man/ntypes.Rd TRONCO/man/oncoprint.Rd TRONCO/man/oncoprint.cbio.Rd TRONCO/man/order.frequency.Rd TRONCO/man/pathway.visualization.Rd TRONCO/man/pheatmap.Rd TRONCO/man/rank.recurrents.Rd TRONCO/man/rename.gene.Rd TRONCO/man/rename.type.Rd TRONCO/man/samples.selection.Rd TRONCO/man/sbind.Rd TRONCO/man/ssplit.Rd TRONCO/man/stage.Rd TRONCO/man/test_dataset.Rd TRONCO/man/test_dataset_no_hypos.Rd TRONCO/man/test_model.Rd TRONCO/man/test_model_kfold.Rd TRONCO/man/trim.Rd TRONCO/man/tronco.bootstrap.Rd TRONCO/man/tronco.caprese.Rd TRONCO/man/tronco.capri.Rd TRONCO/man/tronco.chowliu.Rd TRONCO/man/tronco.edmonds.Rd TRONCO/man/tronco.gabow.Rd TRONCO/man/tronco.kfold.eloss.Rd TRONCO/man/tronco.kfold.posterr.Rd TRONCO/man/tronco.kfold.prederr.Rd TRONCO/man/tronco.pattern.plot.Rd TRONCO/man/tronco.plot.Rd TRONCO/man/tronco.prim.Rd TRONCO/man/view.Rd TRONCO/man/which.samples.Rd
TRONCO/tests
TRONCO/tests/testthat
TRONCO/tests/testthat.R
TRONCO/tests/testthat/test_as_function.R
TRONCO/tests/testthat/test_editing.R
TRONCO/tests/testthat/test_hypotheses.R
TRONCO/tests/testthat/test_statistics.R
TRONCO/tests/testthat/test_tronco.R
TRONCO/tests/testthat/test_visualization.R
TRONCO/vignettes
TRONCO/vignettes/vignette.Rnw

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