as.adj.matrix

A subset of events as of <code>as.events(x)</code>, all by default.

events

A subset of reconstructed models, all by default.

models

Either the prima facie ('pf') or the post-regularization ('fit') matrix, 'fit' by default.

type


Extract the adjacency matrix of a TRONCO model. The matrix is indexed with colnames/rownames which 
represent genotype keys - these can be resolved with function <code>keysToNames</code>. It is possible to
specify a subset of events to build the matrix, a subset of models if multiple reconstruction have
been performed. Also, either the prima facie matrix or the post-regularization matrix can be extracted.



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.

Giulio Caravagna 
Alex Graudenzi alexgraudenzidiscounimibit
Daniele Ramazzotti danieleramazzottidiscounimibit

TRONCO


An R package for the inference of cancer progression models from heterogeneous genomic data

TRONCO, an R package for TRanslational ONCOlogy

as.adj.matrix function

Extract the adjacency matrix of a TRONCO model. The matrix is indexed with colnames/rownames which 
represent genotype keys - these can be resolved with function <code>keysToNames</code>. It is possible to
specify a subset of events to build the matrix, a subset of models if multiple reconstruction have
been performed. Also, either the prima facie matrix or the post-regularization matrix can be extracted.

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as.adj.matrix: as.adj.matrix

Description

Usage

Arguments

Value

Examples