oncokb: OncoKB annotate \ Enables oncokb annotation of MAF, fusions...

View source: R/oncokb.R

oncokbR Documentation

OncoKB annotate \ Enables oncokb annotation of MAF, fusions and CNA files. This is performed using the OncoKB annotator found at https://github.com/oncokb/oncokb-annotator. See details there for file formats.

Description

OncoKB annotate \ Enables oncokb annotation of MAF, fusions and CNA files. This is performed using the OncoKB annotator found at https://github.com/oncokb/oncokb-annotator. See details there for file formats.

Usage

oncokb(
  maf = NULL,
  fusion = NULL,
  cna = NULL,
  token = Sys.getenv("ONCOKB_TOKEN"),
  clin.file = NULL
)

Arguments

maf

A maf file to be annotated

fusion

A fusion file to be annotated

cna

A CNA file to be annotated

token

Required token to access OncoKB API, see https://www.oncokb.org/ for details.

clin.file

Optional dataframe containing the cancer types of the samples to be annotated.

Value

OncoKB annotated files

Examples

## Not run: 
library(gnomeR)
test <- oncokb(maf = mut[1:100,], token = 'YOUR TOKEN')
test$maf_oncokb$oncogenic

## End(Not run)

AxelitoMartin/gnomeR documentation built on April 21, 2022, 3:01 p.m.