import.GISTIC

filter.genes

filter.samples

A parameter to disable/enable verbose messages.

silent

trim


Transform GISTIC scores for CNAs in a TRONCO compliant object. Input can be either a matrix, with columns
for each altered gene and rows for each sample; in this case colnames/rownames mut be provided. If input
is a character an attempt to load a table from file is performed. In this case the input table format
should be constitent with TCGA data for focal CNA; there should hence be: one column for each sample,
one row for each gene, a column Hugo_Symbol with every gene name and a column Entrez_Gene_Id with every
 gene\'s Entrez ID. A valid GISTIC score should be any value of: "Homozygous Loss" (-2), "Heterozygous
 Loss" (-1), "Low-level Gain" (+1), "High-level Gain" (+2).



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

import.GISTIC function

Transform GISTIC scores for CNAs in a TRONCO compliant object. Input can be either a matrix, with columns
for each altered gene and rows for each sample; in this case colnames/rownames mut be provided. If input
is a character an attempt to load a table from file is performed. In this case the input table format
should be constitent with TCGA data for focal CNA; there should hence be: one column for each sample,
one row for each gene, a column Hugo_Symbol with every gene name and a column Entrez_Gene_Id with every
 gene's Entrez ID. A valid GISTIC score should be any value of: "Homozygous Loss" (-2), "Heterozygous
 Loss" (-1), "Low-level Gain" (+1), "High-level Gain" (+2).

import.GISTIC: import.GISTIC

Description

Usage

Arguments

Value

Examples