as.gene

The genes to consider, if NA all available genes are used.

genes

The types of events to consider, if NA all available types are used.

types


Return the genotypes for a certain set of genes and type of events. Input 'x' should be a
TRONCO compliant dataset - see <code>is.compliant</code>. In this case column names are substituted
with events' types.



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.gene function

Return the genotypes for a certain set of genes and type of events. Input 'x' should be a
TRONCO compliant dataset - see <code>is.compliant</code>. In this case column names are substituted
with events' types.

as.gene: as.gene

Description

Usage

Arguments

Value

Examples