cbioportal-api-client

cBio Portal API Client

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

This library can be used programatically or via the command line.

Installation

$ npm install cbioportal-api-client --save

Programmatic Usage

API Reference

import CbioPortal from 'cbioportal-api-client';

const cbioPortal = CbioPortal();

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

cbioPortal.getGeneticProfiles({ cancer_study_id: 'gbm_tcga' })
  .then(response => {
    console.log(response); // Prints array of genetic profiles returned from the 'gbm_tcga' study
  });

Command Line Usage

Note: Requires node.

# global install to use anywhere
$ npm install -g cbioportal-api-client

# print usage info using --help
$ cbioportal-api-client --help

  Usage: cbioportal-api-client [options] [command]


  Commands:

    getCancerStudies               get cancer study meta-data
    getTypesOfCancer               get clinical cancer types
    getGeneticProfiles [options]   get genetic profile data for a cancer study.
    getCaseLists [options]         get case lists stored for a specific cancer study.
    getProfileData [options]       get genomic profile data for one or more genes.

  You can get usage info for specific commands using [command] --help

  Options:

    -h, --help             output usage information
    -V, --version          output the version number
    -f, --format <format>  response format

# example API call, sends JSON formatted response to stdout
$ cbioportal-api-client getProfileData -s gbm_tcga_cnaseq -p gbm_tcga_mutations -g TP53

---

API Reference

Modules

cbioportal-api-client ⇒ cbioPortal

Creates a new cBio Portal API client

cbioportal-api-client/utils/convertResponse ⇒ Promise

Converts tab delimited responses to JSON format

cbioportal-api-client/utils/summarizeAlterations

Exports utility functions for summarizing gene alterations

cbioportal-api-client ⇒ cbioPortal

Creates a new cBio Portal API client

See: cbioPortal

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
  });

• cbioportal-api-client ⇒ cbioPortal
  • ~cbioPortal : Object
    • .getTypesOfCancer() ⇒ Promise
    • .getCancerStudies() ⇒ Promise
    • .getGeneticProfiles(query) ⇒ Promise
    • .getCaseLists(query) ⇒ Promise
    • .getProfileData(query) ⇒ Promise

---

cbioportal-api-client~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 cbioportal-api-client
See: Use CbioPortal() for object creation.

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

---

cbioPortal.getTypesOfCancer() ⇒ Promise

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

Kind: instance method of cbioPortal
Returns: Promise - See fullfills/rejects
Fulfills: Array response data converted from TSV to JSON

---

cbioPortal.getCancerStudies() ⇒ Promise

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

Kind: instance method of cbioPortal
Returns: Promise - See fullfills/rejects
Fulfills: Array response data converted from TSV to JSON

---

cbioPortal.getGeneticProfiles(query) ⇒ Promise

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 - See fullfills/rejects
Fulfills: Array response data converted from TSV to JSON

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

---

cbioPortal.getCaseLists(query) ⇒ Promise

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
Fulfill: JSON formatted response

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

---

cbioPortal.getProfileData(query) ⇒ Promise

Retrieves genomic profile data for one or more genes.

Kind: instance method of cbioPortal
Fulfill: JSON formatted response

Param	Type	Description
query	Object
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

---

cbioportal-api-client/utils/convertResponse ⇒ Promise

Converts tab delimited responses to JSON format

Returns: Promise - Resolves with the response JSON

Param	Type	Description
response	string	TSV string

---

cbioportal-api-client/utils/summarizeAlterations

Exports utility functions for summarizing gene alterations

• cbioportal-api-client/utils/summarizeAlterations
  • .summarizeMutations(mutations) ⇒ Array
  • .summarizeCopyNumberAlterations(copyNumberAlterations) ⇒ Array
  • .summarizeAlterations(response) ⇒ Promise

---

cbioportal-api-client/utils/summarizeAlterations.summarizeMutations(mutations) ⇒ Array

Summarize mutations

Kind: static method of cbioportal-api-client/utils/summarizeAlterations
Returns: Array - Array of summaries

Param	Type	Description
mutations	Array	Array of mutation rows as parsed by this library

---

cbioportal-api-client/utils/summarizeAlterations.summarizeCopyNumberAlterations(copyNumberAlterations) ⇒ Array

Summarize copy number alterations

Kind: static method of cbioportal-api-client/utils/summarizeAlterations
Returns: Array - Array of summaries

Param	Type	Description
copyNumberAlterations	Array	Array of copy number alteration rows as parsed by this library

---

cbioportal-api-client/utils/summarizeAlterations.summarizeAlterations(response) ⇒ Promise

Converts tab delimited responses to JSON format

Kind: static method of cbioportal-api-client/utils/summarizeAlterations
Returns: Promise - Resolves with the response JSON

Param	Type	Description
response	string	TSV string

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