as.pathway

pathway.genes

pathway.name

pathway.color

If TRUE drop the events for the genes in the pathway.

aggregate.pathway

A parameter to disable/enable verbose messages.

silent


Given a cohort and a pathway, return the cohort with events restricted to genes 
involved in the pathway. This might contain a new 'pathway' genotype with an alteration mark if
any of the involved genes are altered.



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.pathway function

Given a cohort and a pathway, return the cohort with events restricted to genes 
involved in the pathway. This might contain a new 'pathway' genotype with an alteration mark if
any of the involved genes are altered.

as.pathway: as.pathway

Description

Usage

Arguments

Value

Examples