oncokb_annotate_maf: Annotate OncoKB levels of evidence

In kpjonsson/annotate-maf: Functional Annotation of Variants in a MAF File

Annotate OncoKB levels of evidence

Description

Adds OncoKB oncogenicity and actionability annotation to VEP-annotated MAF. See URLs below.

Usage

query_oncokb(gene, protein_change, variant_type, start, end,
  cancer_type = "CANCER")

oncokb_annotate_maf(maf, cancer_types = NULL, parallelize = TRUE)

Arguments

gene	Gene.
protein_change	Abbreviated form, e.g. "H1047R".
variant_type	Lower case variant type, e.g. "missense".
start	Genomic start position of variant.
end	Genomic end position of variant.
cancer_type	Oncotree code for cancer type. Can be left blank.
maf	Input MAF.
cancer_types	Data frame with samples mapped to cancer type for accurate levels of actionability.
parallelize	Boolean indicating whether to parallelize annotation, using future backend.

Value

Annotated MAF with columns indicating functionality of mutation and levels of actionability.

Source

oncokb.org

github.com/oncokb/oncokb-annotator

Examples

query_oncokb('PIK3CA', 'H1047R', 'missense')

kpjonsson/annotate-maf documentation built on Nov. 25, 2024, 8:10 a.m.