The R interface to the cBioPortal API Data Service

This section of the documentation lists the functions that allow users to access the cBioPortal API. The main representation of the API can be obtained from the cBioPortal function. The supporting functions listed here give access to specific parts of the API and allow the user to explore the API with individual calls. Many of the functions here are listed for documentation purposes and are recommended for advanced usage only. Users should only need to use the cBioPortalData main function to obtain data.

Usage

cBioPortal(
  hostname = "www.cbioportal.org",
  protocol = "https",
  api. = "/api/v2/api-docs",
  token = character()
)

getStudies(api, buildReport = FALSE)

clinicalData(api, studyId = NA_character_)

molecularProfiles(
  api,
  studyId = NA_character_,
  projection = c("SUMMARY", "ID", "DETAILED", "META")
)

fetchData(
  api,
  studyId,
  molecularProfileIds = NA_character_,
  entrezGeneIds = NULL,
  sampleIds = NULL
)

mutationData(
  api,
  molecularProfileIds = NA_character_,
  entrezGeneIds = NULL,
  sampleIds = NULL
)

molecularData(
  api,
  molecularProfileIds = NA_character_,
  entrezGeneIds = NULL,
  sampleIds = NULL
)

copyNumberData(
  api,
  molecularProfileIds = NA_character_,
  entrezGeneIds = NULL,
  sampleIds = NULL,
  sampleListId = NULL,
  discreteCopyNumberEventType = c("HOMDEL_AND_AMP", "HOMDEL", "AMP", "GAIN", "HETLOSS",
    "DIPLOID", "ALL"),
  projection = c("SUMMARY", "ID", "DETAILED", "META")
)

searchOps(api, keyword)

samplesInSampleLists(api, sampleListIds = NA_character_)

sampleLists(api, studyId = NA_character_)

allSamples(api, studyId = NA_character_)

getSampleInfo(
  api,
  studyId = NA_character_,
  sampleListIds = NULL,
  projection = c("SUMMARY", "ID", "DETAILED", "META")
)

genePanels(api)

getGenePanel(api, genePanelId = NA_character_)

genePanelMolecular(
  api,
  molecularProfileId = NA_character_,
  sampleListId = NULL,
  sampleIds = NULL
)

getGenePanelMolecular(api, molecularProfileIds = NA_character_, sampleIds)

geneTable(api, pageSize = 1000, pageNumber = 0, ...)

queryGeneTable(
  api,
  by = c("entrezGeneId", "hugoGeneSymbol"),
  genes = NA_character_,
  genePanelId = NA_character_
)

getDataByGenes(
  api,
  studyId = NA_character_,
  genes = NA_character_,
  genePanelId = NA_character_,
  by = c("entrezGeneId", "hugoGeneSymbol"),
  molecularProfileIds = NULL,
  sampleListId = NULL,
  sampleIds = NULL,
  ...
)

Arguments

hostname: character(1) The internet location of the service (default: 'www.cbioportal.org')
protocol: character(1) The internet protocol used to access the hostname (default: 'https')
api.: character(1) The directory location of the API protocol within the hostname (default: '/api/v2/api-docs')
token: character(1) The Authorization Bearer token e.g., "63eba81c-2591-4e15-9d1c-fb6e8e51e35d" or a path to text file.
api: An API object of class cBioPortal from the cBioPortal function
buildReport: logical(1) Indicates whether to append the build information to the getStudies() table (default FALSE)
studyId: character(1) Indicates the "studyId" as taken from getStudies
projection: character(1) (default: "SUMMARY") Specify the projection type for data retrieval for details see API documentation
molecularProfileIds: character() A vector of molecular profile IDs
entrezGeneIds: numeric() A vector indicating entrez gene IDs
sampleIds: character() Sample identifiers
sampleListId: character(1) A sample list identifier as obtained from sampleLists()
discreteCopyNumberEventType: character(1) The copy number event type to filter on. Must be one of "HOMDEL_AND_AMP" (default), "HOMDEL", "AMP", "GAIN", "HETLOSS", "DIPLOID", or "ALL"
keyword: character(1) Keyword or pattern for searching through available operations
sampleListIds: character() A vector of 'sampleListId' as obtained from sampleLists
genePanelId: character(1) Identifies the gene panel, as obtained from the genePanels function
molecularProfileId: character(1) Indicates a molecular profile ID
pageSize: numeric(1) The number of rows in the table to return
pageNumber: numeric(1) The pagination page number
...: Additional arguments to lower level API functions
by: character(1) Either 'entrezGeneId' or 'hugoGeneSymbol' for row metadata (default: 'entrezGeneId')
genes: character() Either Entrez gene identifiers or Hugo gene symbols. When included, the 'by' argument indicates the type of identifier provided and 'genePanelId' is ignored. Preference is given to Entrez IDs due to faster query responses.

Value

cBioPortal: An API object of class 'cBioPortal'
cBioPortalData: A data object of class 'MultiAssayExperiment'

API Metadata

getStudies: Obtain a table of studies and associated metadata and optionally include a buildReport status (default FALSE) for each study. When enabled, the 'api_build' and 'pack_build' columns will be added to the table and will show if MultiAssayExperiment objects can be generated for that particular study identifier (studyId). The 'api_build' column corresponds to datasets obtained with cBioPortalData and the 'pack_build' column corresponds to datsets loaded via cBioDataPack.

searchOps - Search through API operations with a keyword

sampleLists - obtain all sampleListIds for a particular studyId

allSamples - obtain all samples within a particular studyId

genePanels - Show all available gene panels

geneTable - Get a table of all genes by 'entrezGeneId' and 'hugoGeneSymbol'

queryGeneTable - Get a table for only the genes or genePanelId of interest. Gene inputs are identified with the by argument

Patient Data

clinicalData - Obtain clinical data for a particular study identifier ('studyId')

Molecular Profiles

molecularProfiles - Produce a molecular profiles dataset for a given study identifier ('studyId')

Molecular Data

fetchData - A convenience function to download both mutation and molecular data with molecularProfileId, entrezGeneIds, and sampleIds

mutationData - Produce a dataset of mutation data using molecularProfileId, entrezGeneIds, and sampleIds

molecularData - Produce a dataset of molecular profile data based on molecularProfileId, entrezGeneIds, and sampleIds

Copy Number Data

copyNumberData - Produce a dataset of copy number data based on molecularProfileId, sampleListId, discreteCopyNumberEventType, and projection

Sample Data

samplesInSampleLists - get all samples associated with a 'sampleListId'

getSampleInfo - Obtain sample metadata for a particular studyId or sampleListId

Gene Panels

getGenePanels - Obtain the gene panel for a particular 'genePanelId'

genePanelMolecular - get gene panel data for a particular molecularProfileId and either a vector of sampleListId or sampleId

getGenePanelMolecular - get gene panel data for multiple molecularProfileIds and a vector of sampleIds

Genes

getDataByGenes - Download data for a number of genes within molecularProfileId indicators, optionally a sampleListId can be provided.

Examples

cbio <- cBioPortal()

getStudies(api = cbio)
#> # A tibble: 485 × 13
#>    name          description publicStudy pmid  citation groups status importDate
#>    <chr>         <chr>       <lgl>       <chr> <chr>    <chr>   <int> <chr>     
#>  1 Acute Lympho… Comprehens… TRUE        2573… Anderss… "PUBL…      0 2024-12-0…
#>  2 Hypodiploid … Whole geno… TRUE        2333… Holmfel… ""          0 2024-12-0…
#>  3 Adenoid Cyst… Targeted S… TRUE        2441… Ross et… "ACYC…      0 2024-12-0…
#>  4 Adenoid Cyst… Whole-geno… TRUE        2686… Rettig … "ACYC…      0 2024-12-0…
#>  5 Adenoid Cyst… WGS of 21 … TRUE        2663… Mitani … "ACYC…      0 2024-12-0…
#>  6 Adenoid Cyst… Whole-geno… TRUE        2682… Drier e… "ACYC"      0 2024-12-0…
#>  7 Adenoid Cyst… Whole exom… TRUE        2377… Stephen… "ACYC…      0 2024-12-0…
#>  8 Acute Lympho… Whole-geno… TRUE        2777… Zhang e… "PUBL…      0 2024-12-0…
#>  9 Appendiceal … Targeted s… TRUE        3649… Michael… "PUBL…      0 2024-12-0…
#> 10 Bladder Canc… Whole exom… TRUE        2690… Al-Ahma… ""          0 2024-12-0…
#> # ℹ 475 more rows
#> # ℹ 5 more variables: allSampleCount <int>, readPermission <lgl>,
#> #   studyId <chr>, cancerTypeId <chr>, referenceGenome <chr>

clinicalData(cbio, "acc_tcga")
#> # A tibble: 92 × 85
#>    patientId    AGE   AJCC_PATHOLOGIC_TUMOR_STAGE ATYPICAL_MITOTIC_FIGURES      
#>    <chr>        <chr> <chr>                       <chr>                         
#>  1 TCGA-OR-A5J1 58    Stage II                    Atypical Mitotic Figures Abse…
#>  2 TCGA-OR-A5J2 44    Stage IV                    Atypical Mitotic Figures Pres…
#>  3 TCGA-OR-A5J3 23    Stage III                   Atypical Mitotic Figures Abse…
#>  4 TCGA-OR-A5J4 23    Stage IV                    Atypical Mitotic Figures Abse…
#>  5 TCGA-OR-A5J5 30    Stage III                   Atypical Mitotic Figures Pres…
#>  6 TCGA-OR-A5J6 29    Stage II                    Atypical Mitotic Figures Abse…
#>  7 TCGA-OR-A5J7 30    Stage III                   Atypical Mitotic Figures Pres…
#>  8 TCGA-OR-A5J8 66    Stage III                   Atypical Mitotic Figures Pres…
#>  9 TCGA-OR-A5J9 22    Stage II                    Atypical Mitotic Figures Abse…
#> 10 TCGA-OR-A5JA 53    Stage IV                    Atypical Mitotic Figures Pres…
#> # ℹ 82 more rows
#> # ℹ 81 more variables: CAPSULAR_INVASION <chr>, CLIN_M_STAGE <chr>,
#> #   CT_SCAN_PREOP_RESULTS <chr>,
#> #   CYTOPLASM_PRESENCE_LESS_THAN_EQUAL_25_PERCENT <chr>,
#> #   DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS <chr>, DFS_MONTHS <chr>,
#> #   DFS_STATUS <chr>, DIFFUSE_ARCHITECTURE <chr>, ETHNICITY <chr>,
#> #   FORM_COMPLETION_DATE <chr>, HISTOLOGICAL_DIAGNOSIS <chr>, …

molecularProfiles(cbio, "acc_tcga")
#> # A tibble: 9 × 8
#>   molecularAlterationType datatype   name     description showProfileInAnalysi…¹
#>   <chr>                   <chr>      <chr>    <chr>       <lgl>                 
#> 1 PROTEIN_LEVEL           LOG2-VALUE Protein… Protein ex… FALSE                 
#> 2 PROTEIN_LEVEL           Z-SCORE    Protein… Protein ex… TRUE                  
#> 3 COPY_NUMBER_ALTERATION  DISCRETE   Putativ… Putative c… TRUE                  
#> 4 COPY_NUMBER_ALTERATION  CONTINUOUS Capped … Capped rel… FALSE                 
#> 5 MUTATION_EXTENDED       MAF        Mutatio… Mutation d… TRUE                  
#> 6 METHYLATION             CONTINUOUS Methyla… Methylatio… FALSE                 
#> 7 MRNA_EXPRESSION         CONTINUOUS mRNA ex… mRNA gene … FALSE                 
#> 8 MRNA_EXPRESSION         Z-SCORE    mRNA ex… mRNA expre… TRUE                  
#> 9 MRNA_EXPRESSION         Z-SCORE    mRNA ex… Log-transf… TRUE                  
#> # ℹ abbreviated name: ¹showProfileInAnalysisTab
#> # ℹ 3 more variables: patientLevel <lgl>, molecularProfileId <chr>,
#> #   studyId <chr>

fetchData(
    api = cbio, studyId = "acc_tcga",
    molecularProfileIds = c(
        "acc_tcga_mutations", "acc_tcga_gistic", "acc_tcga_rppa"
    ),
    entrezGeneIds = 1:1000,
    sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01")
)
#> $acc_tcga_mutations
#> # A tibble: 7 × 27
#>   uniqueSampleKey         uniquePatientKey molecularProfileId sampleId patientId
#>   <chr>                   <chr>            <chr>              <chr>    <chr>    
#> 1 VENHQS1PUi1BNUoxLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 2 VENHQS1PUi1BNUoxLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 3 VENHQS1PUi1BNUoxLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 4 VENHQS1PUi1BNUoxLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 5 VENHQS1PUi1BNUoyLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 6 VENHQS1PUi1BNUoyLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 7 VENHQS1PUi1BNUoyLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> # ℹ 22 more variables: entrezGeneId <int>, studyId <chr>, center <chr>,
#> #   mutationStatus <chr>, validationStatus <chr>, tumorAltCount <int>,
#> #   tumorRefCount <int>, normalAltCount <int>, normalRefCount <int>,
#> #   startPosition <int>, endPosition <int>, referenceAllele <chr>,
#> #   proteinChange <chr>, mutationType <chr>, ncbiBuild <chr>,
#> #   variantType <chr>, keyword <chr>, chr <chr>, variantAllele <chr>,
#> #   refseqMrnaId <chr>, proteinPosStart <int>, proteinPosEnd <int>
#> 
#> $acc_tcga_gistic
#> # A tibble: 64 × 8
#>    uniqueSampleKey        uniquePatientKey molecularProfileId sampleId patientId
#>    <chr>                  <chr>            <chr>              <chr>    <chr>    
#>  1 VENHQS1PUi1BNUoxLTAxO… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#>  2 VENHQS1PUi1BNUoxLTAxO… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#>  3 VENHQS1PUi1BNUoxLTAxO… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#>  4 VENHQS1PUi1BNUoxLTAxO… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#>  5 VENHQS1PUi1BNUoxLTAxO… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#>  6 VENHQS1PUi1BNUoxLTAxO… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#>  7 VENHQS1PUi1BNUoxLTAxO… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#>  8 VENHQS1PUi1BNUoxLTAxO… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#>  9 VENHQS1PUi1BNUoxLTAxO… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#> 10 VENHQS1PUi1BNUoxLTAxO… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#> # ℹ 54 more rows
#> # ℹ 3 more variables: entrezGeneId <int>, studyId <chr>, alteration <int>
#> 
#> $acc_tcga_rppa
#> # A tibble: 27 × 8
#>    uniqueSampleKey     uniquePatientKey entrezGeneId molecularProfileId sampleId
#>    <chr>               <chr>                   <int> <chr>              <chr>   
#>  1 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…           31 acc_tcga_rppa      TCGA-OR…
#>  2 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…           94 acc_tcga_rppa      TCGA-OR…
#>  3 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…          103 acc_tcga_rppa      TCGA-OR…
#>  4 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…          207 acc_tcga_rppa      TCGA-OR…
#>  5 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…          208 acc_tcga_rppa      TCGA-OR…
#>  6 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…          301 acc_tcga_rppa      TCGA-OR…
#>  7 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…          310 acc_tcga_rppa      TCGA-OR…
#>  8 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…          367 acc_tcga_rppa      TCGA-OR…
#>  9 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…          440 acc_tcga_rppa      TCGA-OR…
#> 10 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…          472 acc_tcga_rppa      TCGA-OR…
#> # ℹ 17 more rows
#> # ℹ 3 more variables: patientId <chr>, studyId <chr>, value <dbl>
#> 
mutationData(
    api = cbio,
    molecularProfileIds = "acc_tcga_mutations",
    entrezGeneIds = 1:1000,
    sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01")
)
#> $acc_tcga_mutations
#> # A tibble: 7 × 27
#>   uniqueSampleKey         uniquePatientKey molecularProfileId sampleId patientId
#>   <chr>                   <chr>            <chr>              <chr>    <chr>    
#> 1 VENHQS1PUi1BNUoxLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 2 VENHQS1PUi1BNUoxLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 3 VENHQS1PUi1BNUoxLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 4 VENHQS1PUi1BNUoxLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 5 VENHQS1PUi1BNUoyLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 6 VENHQS1PUi1BNUoyLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> 7 VENHQS1PUi1BNUoyLTAxOm… VENHQS1PUi1BNUo… acc_tcga_mutations TCGA-OR… TCGA-OR-…
#> # ℹ 22 more variables: entrezGeneId <int>, studyId <chr>, center <chr>,
#> #   mutationStatus <chr>, validationStatus <chr>, tumorAltCount <int>,
#> #   tumorRefCount <int>, normalAltCount <int>, normalRefCount <int>,
#> #   startPosition <int>, endPosition <int>, referenceAllele <chr>,
#> #   proteinChange <chr>, mutationType <chr>, ncbiBuild <chr>,
#> #   variantType <chr>, keyword <chr>, chr <chr>, variantAllele <chr>,
#> #   refseqMrnaId <chr>, proteinPosStart <int>, proteinPosEnd <int>
#> 

molecularData(
    api = cbio,
    molecularProfileIds = c("acc_tcga_rna_seq_v2_mrna", "acc_tcga_rppa"),
    entrezGeneIds = 1:100,
    sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01")
)
#> $acc_tcga_rna_seq_v2_mrna
#> # A tibble: 128 × 8
#>    uniqueSampleKey     uniquePatientKey entrezGeneId molecularProfileId sampleId
#>    <chr>               <chr>                   <int> <chr>              <chr>   
#>  1 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…            1 acc_tcga_rna_seq_… TCGA-OR…
#>  2 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…            2 acc_tcga_rna_seq_… TCGA-OR…
#>  3 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…            9 acc_tcga_rna_seq_… TCGA-OR…
#>  4 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…           10 acc_tcga_rna_seq_… TCGA-OR…
#>  5 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…           12 acc_tcga_rna_seq_… TCGA-OR…
#>  6 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…           13 acc_tcga_rna_seq_… TCGA-OR…
#>  7 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…           14 acc_tcga_rna_seq_… TCGA-OR…
#>  8 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…           15 acc_tcga_rna_seq_… TCGA-OR…
#>  9 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…           16 acc_tcga_rna_seq_… TCGA-OR…
#> 10 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…           18 acc_tcga_rna_seq_… TCGA-OR…
#> # ℹ 118 more rows
#> # ℹ 3 more variables: patientId <chr>, studyId <chr>, value <dbl>
#> 
#> $acc_tcga_rppa
#> # A tibble: 2 × 8
#>   uniqueSampleKey      uniquePatientKey entrezGeneId molecularProfileId sampleId
#>   <chr>                <chr>                   <int> <chr>              <chr>   
#> 1 VENHQS1PUi1BNUoyLTA… VENHQS1PUi1BNUo…           31 acc_tcga_rppa      TCGA-OR…
#> 2 VENHQS1PUi1BNUoyLTA… VENHQS1PUi1BNUo…           94 acc_tcga_rppa      TCGA-OR…
#> # ℹ 3 more variables: patientId <chr>, studyId <chr>, value <dbl>
#> 

## obtain molecularProfileId for discrete copy number alteration data
molecularProfiles(cbio, "acc_tcga") |>
    dplyr::filter(
        molecularAlterationType == "COPY_NUMBER_ALTERATION" &
        datatype == "DISCRETE"
    )
#> # A tibble: 1 × 8
#>   molecularAlterationType datatype name       description showProfileInAnalysi…¹
#>   <chr>                   <chr>    <chr>      <chr>       <lgl>                 
#> 1 COPY_NUMBER_ALTERATION  DISCRETE Putative … Putative c… TRUE                  
#> # ℹ abbreviated name: ¹showProfileInAnalysisTab
#> # ℹ 3 more variables: patientLevel <lgl>, molecularProfileId <chr>,
#> #   studyId <chr>

copyNumberData(
    api = cbio,
    molecularProfileIds = "acc_tcga_gistic",
    entrezGeneIds = 25,
    sampleListId = "acc_tcga_all"
)
#> $acc_tcga_gistic
#> # A tibble: 3 × 8
#>   uniqueSampleKey         uniquePatientKey molecularProfileId sampleId patientId
#>   <chr>                   <chr>            <chr>              <chr>    <chr>    
#> 1 VENHQS1PUi1BNUo0LTAxOm… VENHQS1PUi1BNUo… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#> 2 VENHQS1PUi1BNUsyLTAxOm… VENHQS1PUi1BNUs… acc_tcga_gistic    TCGA-OR… TCGA-OR-…
#> 3 VENHQS1QSy1BNUhBLTAxOm… VENHQS1QSy1BNUh… acc_tcga_gistic    TCGA-PK… TCGA-PK-…
#> # ℹ 3 more variables: entrezGeneId <int>, studyId <chr>, alteration <int>
#> 

searchOps(api = cbio, keyword = "molecular")
#>  [1] "fetchGenePanelDataInMultipleMolecularProfilesUsingPOST"   
#>  [2] "getGenericAssayDataInMolecularProfileUsingGET"            
#>  [3] "fetchGenericAssayDataInMultipleMolecularProfilesUsingPOST"
#>  [4] "fetchGenericAssayDataInMolecularProfileUsingPOST"         
#>  [5] "fetchMolecularDataInMultipleMolecularProfilesUsingPOST"   
#>  [6] "getAllMolecularProfilesUsingGET"                          
#>  [7] "fetchMolecularProfilesUsingPOST"                          
#>  [8] "getMolecularProfileUsingGET"                              
#>  [9] "getDiscreteCopyNumbersInMolecularProfileUsingGET"         
#> [10] "fetchDiscreteCopyNumbersInMolecularProfileUsingPOST"      
#> [11] "getAllMolecularDataInMolecularProfileUsingGET"            
#> [12] "fetchAllMolecularDataInMolecularProfileUsingPOST"         
#> [13] "getMutationsInMolecularProfileBySampleListIdUsingGET"     
#> [14] "fetchMutationsInMolecularProfileUsingPOST"                
#> [15] "fetchMutationsInMultipleMolecularProfilesUsingPOST"       
#> [16] "getAllMolecularProfilesInStudyUsingGET"                   

samplesInSampleLists(
    api = cbio,
    sampleListIds = c("acc_tcga_rppa", "acc_tcga_cnaseq")
)
#> CharacterList of length 2
#> [["acc_tcga_cnaseq"]] TCGA-OR-A5J1-01 TCGA-OR-A5J2-01 ... TCGA-PK-A5HC-01
#> [["acc_tcga_rppa"]] TCGA-OR-A5J2-01 TCGA-OR-A5J3-01 ... TCGA-PK-A5HA-01

sampleLists(api = cbio, studyId = "acc_tcga")
#> # A tibble: 9 × 5
#>   category                                name  description sampleListId studyId
#>   <chr>                                   <chr> <chr>       <chr>        <chr>  
#> 1 all_cases_with_mrna_rnaseq_data         Samp… Samples wi… acc_tcga_rn… acc_tc…
#> 2 all_cases_in_study                      All … All sample… acc_tcga_all acc_tc…
#> 3 all_cases_with_cna_data                 Samp… Samples wi… acc_tcga_cna acc_tc…
#> 4 all_cases_with_mutation_and_cna_data    Samp… Samples wi… acc_tcga_cn… acc_tc…
#> 5 all_cases_with_mutation_and_cna_and_mr… Comp… Samples wi… acc_tcga_3w… acc_tc…
#> 6 all_cases_with_methylation_data         Samp… Samples wi… acc_tcga_me… acc_tc…
#> 7 all_cases_with_methylation_data         Samp… Samples wi… acc_tcga_me… acc_tc…
#> 8 all_cases_with_rppa_data                Samp… Samples pr… acc_tcga_rp… acc_tc…
#> 9 all_cases_with_mutation_data            Samp… Samples wi… acc_tcga_se… acc_tc…

genePanels(cbio)
#> # A tibble: 64 × 2
#>    description                                                       genePanelId
#>    <chr>                                                             <chr>      
#>  1 Targeted (27 cancer genes) sequencing of adenoid cystic carcinom… ACYC_FMI_27
#>  2 Targeted panel of 232 genes.                                      Agilent    
#>  3 Targeted panel of 8 genes.                                        AmpliSeq   
#>  4 ARCHER-HEME gene panel (199 genes)                                ARCHER-HEM…
#>  5 ARCHER-SOLID Gene Panel (62 genes)                                ARCHER-SOL…
#>  6 Targeted sequencing of various tumor types via bait v3.           bait_v3    
#>  7 Targeted sequencing of various tumor types via bait v4.           bait_v4    
#>  8 Targeted sequencing of various tumor types via bait v5.           bait_v5    
#>  9 Targeted panel of 387 cancer-related genes.                       bcc_unige_…
#> 10 Research (CMO) IMPACT-Heme gene panel version 3.                  HemePACT_v3
#> # ℹ 54 more rows

getGenePanel(cbio, "AmpliSeq")
#> # A tibble: 8 × 2
#>   entrezGeneId hugoGeneSymbol
#>          <int> <chr>         
#> 1       171023 ASXL1         
#> 2         1788 DNMT3A        
#> 3         3417 IDH1          
#> 4         3418 IDH2          
#> 5        23451 SF3B1         
#> 6         6427 SRSF2         
#> 7         7157 TP53          
#> 8         7307 U2AF1         

queryGeneTable(api = cbio, by = "entrezGeneId", genes = 7157)
#> # A tibble: 1 × 3
#>   entrezGeneId hugoGeneSymbol type          
#>          <int> <chr>          <chr>         
#> 1         7157 TP53           protein-coding

getDataByGenes(
    api = cbio,
    studyId = "acc_tcga",
    genes = 1,
    by = "entrezGeneId",
    molecularProfileIds = "acc_tcga_rna_seq_v2_mrna",
    sampleListId = "acc_tcga_rna_seq_v2_mrna"
)
#> $acc_tcga_rna_seq_v2_mrna
#> # A tibble: 79 × 10
#>    uniqueSampleKey     uniquePatientKey entrezGeneId molecularProfileId sampleId
#>    <chr>               <chr>                   <int> <chr>              <chr>   
#>  1 VENHQS1PUi1BNUoxLT… VENHQS1PUi1BNUo…            1 acc_tcga_rna_seq_… TCGA-OR…
#>  2 VENHQS1PUi1BNUoyLT… VENHQS1PUi1BNUo…            1 acc_tcga_rna_seq_… TCGA-OR…
#>  3 VENHQS1PUi1BNUozLT… VENHQS1PUi1BNUo…            1 acc_tcga_rna_seq_… TCGA-OR…
#>  4 VENHQS1PUi1BNUo1LT… VENHQS1PUi1BNUo…            1 acc_tcga_rna_seq_… TCGA-OR…
#>  5 VENHQS1PUi1BNUo2LT… VENHQS1PUi1BNUo…            1 acc_tcga_rna_seq_… TCGA-OR…
#>  6 VENHQS1PUi1BNUo3LT… VENHQS1PUi1BNUo…            1 acc_tcga_rna_seq_… TCGA-OR…
#>  7 VENHQS1PUi1BNUo4LT… VENHQS1PUi1BNUo…            1 acc_tcga_rna_seq_… TCGA-OR…
#>  8 VENHQS1PUi1BNUo5LT… VENHQS1PUi1BNUo…            1 acc_tcga_rna_seq_… TCGA-OR…
#>  9 VENHQS1PUi1BNUpBLT… VENHQS1PUi1BNUp…            1 acc_tcga_rna_seq_… TCGA-OR…
#> 10 VENHQS1PUi1BNUpCLT… VENHQS1PUi1BNUp…            1 acc_tcga_rna_seq_… TCGA-OR…
#> # ℹ 69 more rows
#> # ℹ 5 more variables: patientId <chr>, studyId <chr>, value <dbl>,
#> #   hugoGeneSymbol <chr>, type <chr>
#>