cbioportal-api-client

cBio Portal API Client

cBio Portal API client. Parses tab separated responses into JSON format and works in node and also in the browser via a module loader such as Webpack.

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API Reference

• cbioportal-api-client
  • module.exports(config) ⇒ cbioPortal ⏏
    • static
      • .convertResponse(response) ⇒ Promise
    • inner
      • ~cbioPortal : Object
        • .getTypesOfCancer() ⇒ Promise
        • .getCancerStudies() ⇒ Promise
        • .getGeneticProfiles(query) ⇒ Promise(data)
        • .getCaseLists(query) ⇒ Promise(data)
        • .getProfileData() ⇒ Promise(data)

module.exports(config) ⇒ cbioPortal ⏏

Creates a new cBio Portal API client

Kind: Exported function

Param	Type	Description
config	Object	Configuration options object.
config.includeRaw	Boolean	Include the raw TSV response

Example
Basic usage:

import CbioPortal from 'cbioportal-api-client';

const cbioPortal = CbioPortal();

cbioPortal.getCancerStudies()
  .then(response => {
    console.log(response); // Prints array of cancer studies returned from API
  });

module.exports.convertResponse(response) ⇒ Promise

Converts tab delimited responses to JSON format

Kind: static method of module.exports
Returns: Promise - Resolves with the response JSON

Param	Type	Description
response	string	TSV string

module.exports~cbioPortal : Object

cbioPortal API Object Prototype. Used as the object prototype when creating an API client object via the module factory method.

Kind: inner constant of module.exports
See: Use CbioPortal() for object creation.

• ~cbioPortal : Object
  • .getTypesOfCancer() ⇒ Promise
  • .getCancerStudies() ⇒ Promise
  • .getGeneticProfiles(query) ⇒ Promise(data)
  • .getCaseLists(query) ⇒ Promise(data)
  • .getProfileData() ⇒ Promise(data)

cbioPortal.getTypesOfCancer() ⇒ Promise

Retrieves a list of all the clinical types of cancer stored on the server.

Kind: instance method of cbioPortal
Returns: Promise - resolves with JSON data

cbioPortal.getCancerStudies() ⇒ Promise

Retrieves meta-data regarding cancer studies stored on the server.

Kind: instance method of cbioPortal
Returns: Promise - resolves with JSON data

cbioPortal.getGeneticProfiles(query) ⇒ Promise(data)

Retrieves meta-data regarding all genetic profiles, e.g. mutation or copy number profiles, stored about a specific cancer study.

Kind: instance method of cbioPortal
Returns: Promise(data) - resolves with JSON data

Param	Type	Description
query	Object
query.cancer_study_id	string	Cancer study ID

cbioPortal.getCaseLists(query) ⇒ Promise(data)

Retrieves meta-data regarding all case lists stored about a specific cancer study.

For example, a within a particular study, only some cases may have sequence data, and another subset of cases may have been sequenced and treated with a specific therapeutic protocol.

Multiple case lists may be associated with each cancer study, and this method enables you to retrieve meta-data regarding all of these case lists.

Kind: instance method of cbioPortal

Param	Type	Description
query	Object
query.cancer_study_id	string	Cancer study ID

cbioPortal.getProfileData() ⇒ Promise(data)

Retrieves genomic profile data for one or more genes.

Kind: instance method of cbioPortal

Param	Type	Description
options.case_set_id	string	A unique ID used to identify the case list ID in subsequent interface calls. This is a human readable ID. For example, "gbm_all" identifies all cases profiles in the TCGA GBM study.
options.genetic_profile_id	Array.<string> | string	One or more genetic profile IDs
options.gene_list	Array.<string> | string	One or more genes, specified as HUGO Gene Symbols or Entrez Gene IDs