cgdsr (version 1.2.3)

cgdsr-getCancerStudies: Get available cancer studies available in CGDS

Description

Queries the CGDS API and returns available cancer studies. Input is a CGDS object and output is a data.matrix with information regarding the different cancer studies.

Usage

## S3 method for class 'CGDS':
getCancerStudies(x, ...)

Arguments

x

A CGDS object (required)

...

Not used.

Value

• A data.frame with three colums:
  1. cancer_study_id: unique ID used to identify the cancer study in subsequent interface calls. This is a human readable ID.
  2. name: short name of the cancer type.
  3. description: short description of the cancer type, describing the source of study.

References

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

See Also

cgdsr,CGDS,getGeneticProfiles,getCaseLists

Examples

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

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]