as.confidence

A vector with any of 'tp', 'pr', 'hg', 'npb', 'pb', 'sb', 'eloss', 'prederr' or 'posterr'.

conf

The name of the models to extract, all by default.

models


Return confidence information for a TRONCO model. Available information are: temporal priority (tp), 
probability raising (pr), hypergeometric test (hg), parametric (pb), non parametric (npb) or 
statistical (sb) bootstrap, entropy loss (eloss), prediction error (prederr).
Confidence is available only once a model has been reconstructed with any of the algorithms implemented
in TRONCO. If more than one model has been reconstructed - for instance via multiple regularizations - 
confidence information is appropriately nested. The requested confidence is specified via 
vector parameter <code>conf</code>.



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.confidence function

Return confidence information for a TRONCO model. Available information are: temporal priority (tp), 
probability raising (pr), hypergeometric test (hg), parametric (pb), non parametric (npb) or 
statistical (sb) bootstrap, entropy loss (eloss), prediction error (prederr).
Confidence is available only once a model has been reconstructed with any of the algorithms implemented
in TRONCO. If more than one model has been reconstructed - for instance via multiple regularizations - 
confidence information is appropriately nested. The requested confidence is specified via 
vector parameter <code>conf</code>.

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as.confidence: as.confidence

Description

Usage

Arguments

Value

Examples