R/MATLAB Packages

CGDS-R Package

Description

The CGDS-R package provides a basic set of functions for querying the Cancer Genomic Data Server (CGDS) via the R platform for statistical computing.

Maintained by Anders Jacobsen at the Computational Biology Center, MSKCC.

Documentation

Installation

  1. The CDGS-R package currently only works with R Version 2.12 or higher.

  2. Then install the cgds-R package from within R:

    install.packages('cgdsr')

Example usage

# Create CGDS object
mycgds = CGDS("http://www.cbioportal.org/public-portal/")

test(mycgds)

# Get list of cancer studies at server
getCancerStudies(mycgds)

# Get available case lists (collection of samples) for a given cancer study
mycancerstudy = getCancerStudies(mycgds)[2,1]
mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1]

# Get available genetic profiles
mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[4,1]

# Get data slices for a specified list of genes, genetic profile and case list
getProfileData(mycgds,c('BRCA1','BRCA2'),mygeneticprofile,mycaselist)

# Get clinical data for the case list
myclinicaldata = getClinicalData(mycgds,mycaselist)

# documentation
help('cgdsr')
help('CGDS')

MATLAB CGDS Cancer Genomics Toolbox

Description

This toolbox provides direct access to cancer genomics data from within the MATLAB environment. The toolbox will query the Cancer Genomics Data Server Web API, and return data in a structured format.

Maintained by Erik Larsson at the Computational Biology Center, MSKCC.

A tutorial ('showdemo cgdstutorial') makes it easy to get started.

Download

CGDS Toolbox @ MATLAB Central

Documentation

Complete CGDS Tutorial

Example Usage

Like the R package, the CGDS MATLAB toolbox provides a set of functions for direct retrieval of portal data from within the MATLAB (MathWorks Inc.) environment. Each toolbox function has a direct counterpart in the CGDS Web API. Data is returned as structured arrays, in a format that is easy to interpret and ready for subsequent visualization and statistical analysis.

An included tutorial ("showdemo cgdstutorial") shows how to use all the functions, as well as how to make basic plots.

% Get started by adding the CGDS toolbox directory to the path (this will depend
% on install location) and setting the server URL
addpath('/MATLAB/cgds');
cgdsURL = 'http://www.cbioportal.org/public-portal';

% Show toolbox help ('helpwin cgds' will open in the Help window)
help cgds;

% Get list of cancer studies at server
cancerStudies = getcancerstudies(cgdsURL);

% Get available genetic profiles for a given cancer type (GBM below)
geneticProfiles = getgeneticprofiles(cgdsURL, cancerStudies.cancerStudyId{2});

% Get available case lists (collections of samples)
caseLists = getcaselists(cgdsURL, cancerStudies.cancerStudyId{2});

% Get multiple types of genetic profile data for p53 in GBM
profileData = getprofiledata(cgdsURL, caseLists.caseListId{2}, ...
                            geneticProfiles.geneticProfileId([3 4]), ...
                            'TP53', true);

% Plot mRNA levels as a function of copy number status
boxplot(profileData.data(2,:),profileData.data(1,:));
title('TP53'); xlabel('Copy-number status'); ylabel('mRNA level');

% Get clinical data for all patients in a given case list
clinicalData = getclinicaldata(cgdsURL, caseLists.caseListId{2});

% Run a function in non-verbose mode
cancerStudies = getcancerstudies(cgdsURL, 'silent');