get_oncokb_response: get_oncokb_response

In mskilab/casereport: casereport: Whole-genome + transcription based report for cancer genomes

get_oncokb_response

Description

Using httr to query genomic changes on OncoKB in accordance with the web API specification in https://www.oncokb.org/swagger-ui/index.html .

Usage

get_oncokb_response(
  variants.dt,
  oncokb.token,
  oncokb.url = "https://www.oncokb.org/api/v1/annotate",
  reference = "GRCh37"
)

Arguments

variants.dt	data.table with the variants to query. As a minimum, must contain the following columns: seqnames, start, end, REF, ALT.
oncokb.token	a token to use when querying OncoKB. If you don't have a token, you must first obtain one from: https://www.oncokb.org/apiAccess

Value

list of response object. Response objects can be parsed using httr (for example: httr::content).

Author(s)

Alon Shaiber

mskilab/casereport documentation built on Oct. 19, 2022, 3 a.m.