tronco.capri

data

Parameter to define to heuristic search to be performed. Hill Climbing and Tabu search are currently available.

command

Select the regularization for the likelihood estimation, e.g., BIC, AIC.

regularization

A parameter to disable/enable the estimation of the error rates give the reconstructed model.

do.boot

Number of bootstrap sampling (with rejection) to be performed when estimating the selective advantage scores.

nboot

Pvalue to accept/reject the valid selective advantage relations.

pvalue

Minimum number of bootstrap sampling to be performed.

min.boot

A parameter to disable/enable the minimum number of bootstrap sampling required besides nboot if any sampling is rejected.

min.stat

Initial seed for the bootstrap random sampling.

boot.seed

A parameter to disable/enable verbose messages.

silent


Reconstruct a progression model using CAPRI algorithm



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

tronco.capri function

Reconstruct a progression model using CAPRI algorithm

tronco.capri: tronco capri

Description

Usage

Arguments

Value

Examples