cbio.query

cbio.study

cbio.dataset

cbio.profile

genes

String containing filename for RData output. If NA no output will be provided

file


Wrapper for the CGDS package to query the Cbio portal. This can work either automatically, if one
sets <code>cbio.study</code>, <code>cbio.dataset</code> or <code>cbio.profile</code>, or interactively otherwise. A
list of genes to query with less than 900 entries should be provided. This function returns a list
with two dataframe: the gentic profile required and clinical data for the Cbio study. Output is also
saved to disk as Rdata file. See also http://www.cbioportal.org.



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

cbio.query function

Wrapper for the CGDS package to query the Cbio portal. This can work either automatically, if one
sets <code>cbio.study</code>, <code>cbio.dataset</code> or <code>cbio.profile</code>, or interactively otherwise. A
list of genes to query with less than 900 entries should be provided. This function returns a list
with two dataframe: the gentic profile required and clinical data for the Cbio study. Output is also
saved to disk as Rdata file. See also http://www.cbioportal.org.

cbio.query: cbio.query

Description

Usage

Arguments

Value