cBioPortal: The R interface to the cBioPortal API Data Service

In waldronlab/MultiAssayExperimentData: Exposes and Makes Available Data from the cBioPortal Web Resources

The R interface to the cBioPortal API Data Service

Description

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)

clinicalData(cbio, "acc_tcga")

molecularProfiles(cbio, "acc_tcga")

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")
)
mutationData(
    api = cbio,
    molecularProfileIds = "acc_tcga_mutations",
    entrezGeneIds = 1:1000,
    sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01")
)

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")
)

## obtain molecularProfileId for discrete copy number alteration data
molecularProfiles(cbio, "acc_tcga") |>
    dplyr::filter(
        molecularAlterationType == "COPY_NUMBER_ALTERATION" &
        datatype == "DISCRETE"
    )

copyNumberData(
    api = cbio,
    molecularProfileIds = "acc_tcga_gistic",
    entrezGeneIds = 25,
    sampleListId = "acc_tcga_all"
)

searchOps(api = cbio, keyword = "molecular")

samplesInSampleLists(
    api = cbio,
    sampleListIds = c("acc_tcga_rppa", "acc_tcga_cnaseq")
)

sampleLists(api = cbio, studyId = "acc_tcga")

genePanels(cbio)

getGenePanel(cbio, "AmpliSeq")

queryGeneTable(api = cbio, by = "entrezGeneId", genes = 7157)

getDataByGenes(
    api = cbio,
    studyId = "acc_tcga",
    genes = 1,
    by = "entrezGeneId",
    molecularProfileIds = "acc_tcga_rna_seq_v2_mrna",
    sampleListId = "acc_tcga_rna_seq_v2_mrna"
)

waldronlab/MultiAssayExperimentData documentation built on Feb. 16, 2025, 4:38 a.m.