oncokbR

{oncokbR} allows you to annotate genomic data sets using MSK’s OncoKB Precision Oncology Knowledge Base directly in R. The package wraps existing OncoKB API endpoints so R users can easily leverage the existing API to annotate data on mutations, copy number alterations and fusions.

This package is compatible with oncoKB data v3.16, but is subject to change as new versions are released. For more information on oncoKB, see [Chakravarty et al. 2017[(https://ascopubs.org/doi/full/10.1200/PO.17.00011).

Gao et al. Sci. Signal. 2013 Cerami et al. Cancer Discov. 2012

Installation

You can install the development version of oncokbR like so:

remotes::install_github('karissawhiting/oncokbR')

Annotate Data

Annotate Mutations:

library(oncokbR)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

Annotate MAF data with tumor type indicated for annotations on oncogenicity and oncoKB treatment levels:

blca_mutation <- oncokbR::blca_mutation %>%
  mutate(tumor_type = "BLCA")

annotated_tt <- annotate_mutations(mutations = blca_mutation[1:50,])

annotated_tt %>%
  select(oncogenic) %>% 
  table()
#> oncogenic
#> Likely Oncogenic        Oncogenic          Unknown 
#>                4                1               45

annotated_tt %>%
  select(treatments_level ) %>% 
  table()
#> treatments_level
#> LEVEL_3B 
#>        1

You can also annotated with no tumor type data for oncogenicity only:

blca_mutation <- oncokbR::blca_mutation

annotated_no_tt <- annotate_mutations(mutations = blca_mutation[1:50,])
#> ℹ No "tumor_type" found in data. No treatment-level annotations will be returned.

annotated_no_tt %>%
  select(oncogenic) %>% table()
#> oncogenic
#> Likely Oncogenic        Oncogenic          Unknown 
#>                4                1               45

Annotate CNA:

blca_cna <- blca_cna %>%
  mutate(tumor_type = "BLCA")


annotated <- annotate_cna(blca_cna[1:10,])
table(annotated$oncogenic)
#> 
#> Likely Oncogenic        Oncogenic          Unknown 
#>                3                6                1

Annotate Structural Variants:

blca_sv <- blca_sv %>%
  mutate(tumor_type = "BLCA")


annotated <- annotate_sv(blca_sv[1:10,])
table(annotated$oncogenic)
#> 
#> Likely Oncogenic        Oncogenic          Unknown 
#>                6                3                1

inodb / oncokbR