A class for representing the oncoKB API protocol

The oncoKB class is a representation of the oncoKB API protocol that directly inherits from the Service class in the AnVIL package. For more information, see the AnVIL package.

Usage

# S4 method for class 'oncoKB'
operations(x, ..., .deprecated = FALSE)

Arguments

x

A Service instance or API representation as given by the oncoKB function.

...

additional arguments passed to methods or, for operations,Service-method, to the internal get_operation() function.

.deprecated

optional logical(1) include deprecated operations?

Value

An oncoKB class instance.

Details

This class takes the static API as provided at https://www.oncoKB.org/api/api-docs and creates an R object with the help from underlying infrastructure (i.e., rapiclient and AnVIL) to give the user a unified representation of the API specification provided by the oncoKB group. Users are not expected to interact with this class other than to use it as input to the functionality provided by the rest of the package.

Functions

• operations(oncoKB):

Slots

api_header

named character() vector passed on to the .headers argument in add_headers()

See also

oncoKB, Service

Examples

oncoKB()
#> service: oncoKB
#> host: www.oncokb.org
#> tags(); use oncokb$<tab completion>:
#> # A tibble: 20 × 3
#>    tag          operation                                       summary         
#>    <chr>        <chr>                                           <chr>           
#>  1 Annotations  annotateCopyNumberAlterationsGetUsingGET_1      annotateCopyNum…
#>  2 Annotations  annotateCopyNumberAlterationsPostUsingPOST_1    annotateCopyNum…
#>  3 Annotations  annotateMutationsByGenomicChangeGetUsingGET_1   annotateMutatio…
#>  4 Annotations  annotateMutationsByGenomicChangePostUsingPOST_1 annotateMutatio…
#>  5 Annotations  annotateMutationsByHGVSgGetUsingGET_1           annotateMutatio…
#>  6 Annotations  annotateMutationsByHGVSgPostUsingPOST_1         annotateMutatio…
#>  7 Annotations  annotateMutationsByProteinChangeGetUsingGET_1   annotateMutatio…
#>  8 Annotations  annotateMutationsByProteinChangePostUsingPOST_1 annotateMutatio…
#>  9 Annotations  annotateStructuralVariantsGetUsingGET_1         annotateStructu…
#> 10 Annotations  annotateStructuralVariantsPostUsingPOST_1       annotateStructu…
#> 11 Cancer Genes utilsAllCuratedGenesGetUsingGET_1               utilsAllCurated…
#> 12 Cancer Genes utilsAllCuratedGenesTxtGetUsingGET_1            utilsAllCurated…
#> 13 Cancer Genes utilsCancerGeneListGetUsingGET_1                utilsCancerGene…
#> 14 Cancer Genes utilsCancerGeneListTxtGetUsingGET_1             utilsCancerGene…
#> 15 Info         infoGetUsingGET_1                               infoGet         
#> 16 Levels       levelsDiagnosticGetUsingGET_1                   levelsDiagnosti…
#> 17 Levels       levelsGetUsingGET_1                             levelsGet       
#> 18 Levels       levelsPrognosticGetUsingGET_1                   levelsPrognosti…
#> 19 Levels       levelsResistanceGetUsingGET_1                   levelsResistanc…
#> 20 Levels       levelsSensitiveGetUsingGET_1                    levelsSensitive…
#> tag values:
#>   Annotations, Cancer Genes, Info, Levels
#> schemas():
#>   AnnotateMutationByGenomicChangeQuery, ParsedGenomeNexusVersion,
#>   Query, ApiHttpError, ParsedVersionInfo
#>   # ... with 25 more elements