cgdsr-CGDS {cgdsr}R Documentation

Construct a CGDS connection object

Description

Creates a CGDS connection object from a CGDS endpoint URL. This object must be passed on to the methods which query the server.

Usage

CGDS(url,verbose=FALSE,ploterrormsg='',token=NULL)

Arguments

url

A CGDS URL (required).

verbose

A boolean variable specifying verbose output (default FALSE)

ploterrormsg

An optional message to display in plots if an error occurs (default ”)

token

An optional 'Authorization: Bearer' token to connect to cBioPortal instances that require authentication (default NULL)

Value

A CGDS connection object. This object must be passed on to the methods which query the server.

Author(s)

<jacobsen@cbio.mskcc.org>

References

cBio Cancer Genomics Portal: http://www.cbioportal.org/

See Also

cgdsr,getCancerStudies,getGeneticProfiles,getCaseLists,getProfileData

Examples

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

# Test the CGDS endpoint URL using a few simple API tests
test(mycgds) 

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

[Package cgdsr version 1.3.0 Index]