In LiNk-NY/oncoKBData: A package to access the oncoKB web API

knitr::opts_chunk$set(cache = TRUE)

oncoKBData

The aim of the package is to expose the OncoKB API through an R client. This vignette demonstrates public API access. To learn more about the OncoKB database, visit https://www.oncokb.org.

Installation

To get the development version of oncoKBData use:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("waldronlab/oncoKBData")

Package Load

library(oncoKBData)
library(S4Vectors)

Introduction

The oncoKBData aims to provide access to the OncoKB API via the public API. Access is also possible with a licensed token.

API representation

In order to use the OncoKB API, we must instantiate an API object as provided by the r CRANpkg("rapiclient") and r Biocpkg("AnVIL") packages.

oncokb <- oncoKB()

Note that for private API access, users must change the api. argument in the oncoKB function.

Operations

Check available tags, operations, and descriptions as a tibble:

tags(oncokb)
head(tags(oncokb)$operation)

Note. The annotations API access requires a token.

Levels of Evidence

To retrieve the levels of evidence for all types (i.e., 'therapeutic', 'diagnostic', 'prognostic', and 'FDA') run the levelsOfEvidence function.

(loe <- levelsOfEvidence(oncokb))

It will return a DataFrame with important metadata:

names(metadata(loe))

metadata(loe)["oncoTreeVersion"]

metadata(loe)[["apiVersion"]]

Gene tables

The API allows retrieval of curated genes where there is a single gene per observation:

curatedGenes(oncokb)

and a long list of genes associated with cancer where there can be multiple entries for the same hugoSymbol due to multiple geneAliases:

cancerGeneList(oncokb)

Session Information

sessionInfo()

LiNk-NY/oncoKBData documentation built on Oct. 1, 2024, 1:57 p.m.