Package 'oncoKBData'

Obtain the OncoKB cancer gene list

Description

Obtain the OncoKB cancer gene list

Usage

cancerGeneList(api)

Arguments

api	An OncoKB API instance as returned by oncoKB()

Value

A long tibble of genes with additional columns

Examples

oncokb <- oncoKB()
cancerGeneList(oncokb)

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Get a table of curated oncogenes

Description

Get a table of curated oncogenes

Usage

curatedGenes(api, includeEvidence = TRUE)

Arguments

api	An OncoKB API instance as returned by oncoKB()
includeEvidence	logical(1) Whether to include additional data in the summary and background columns (default: TRUE)

Value

A tibble of curated oncogenes

Examples

oncokb <- oncoKB()
curatedGenes(oncokb)

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Get the Levels of Evidence Tables from OncoKB

Description

The levels of evidence table is an S4Vectors DataFrame that includes metadata consisting of app, api, data, and oncoTree version tags which were used to generate the table.

Usage

levelsOfEvidence(api)

Arguments

api	An OncoKB API instance as returned by oncoKB()

Value

A DataFrame with metadata

Examples

oncokb <- oncoKB()
levelsOfEvidence(oncokb)

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The R interface to the oncoKB API Data Service

Description

This section of the documentation lists the functions that allow users to access the oncoKB API. The main representation of the API can be obtained from the oncoKB function. The supporting functions listed here give access to specific parts of the API and allow the user to explore the API with individual calls.

Usage

oncoKB(
  hostname = "www.oncokb.org",
  protocol = "https",
  api. = .DEMO_ENDPOINT,
  token = character()
)

Arguments

hostname	character(1) The internet location of the service (default: 'www.cbioportal.org')
protocol	character(1) The internet protocol used to access the hostname (default: 'https')
api.	character(1) The directory location of the API protocol within the hostname (default: '/api/api-docs')
token	character(1) The Authorization Bearer token e.g., "63eba81c-2591-4e15-9d1c-fb6e8e51e35d" or a path to text file.

Value

oncoKB: An API object of class 'oncoKB'

Examples

oncokb <- oncoKB()

## Authorization: Bearer token as a file
if (interactive())
  oncoKB(token = "~/onco_token.txt")

names(operations(oncokb))

---

A class for representing the oncoKB API protocol

Description

The oncoKB class is a representation of the oncoKB API protocol that directly inherits from the Service class in the AnVIL package. For more information, see the AnVIL package.

Usage

## S4 method for signature 'oncoKB'
operations(x, ..., .deprecated = FALSE)

Arguments

x	A Service instance or API representation as given by the oncoKB function.
...	additional arguments passed to methods or, for ⁠operations,Service-method⁠, to the internal get_operation() function.
.deprecated	optional logical(1) include deprecated operations?

Details

This class takes the static API as provided at https://www.oncoKB.org/api/api-docs and creates an R object with the help from underlying infrastructure (i.e., rapiclient and AnVIL) to give the user a unified representation of the API specification provided by the oncoKB group. Users are not expected to interact with this class other than to use it as input to the functionality provided by the rest of the package.

Value

An oncoKB class instance.

Functions

• operations(oncoKB):

Slots

api_header

⁠named character()⁠ vector passed on to the .headers argument in add_headers()

See Also

oncoKB, Service

Examples

oncoKB()

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