R/oncokb.R
oncokb.Rd
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.
oncokb( maf = NULL, fusion = NULL, cna = NULL, token = Sys.getenv("ONCOKB_TOKEN"), clin.file = NULL )
maf | A maf file to be annotated |
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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. |
OncoKB annotated files