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,
  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
)

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(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
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
sampleListId	character(1) A sample list identifier as obtained from 'sampleLists()“
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'

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 'molecularProfileId's 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)

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

## obtain clinical data
acc_clin <- clinicalData(api = cbio, studyId = "acc_tcga")
acc_clin

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

genePanels(cbio)

(gp <- getGenePanel(cbio, "AmpliSeq"))

muts <- mutationData(
    api = cbio,
    molecularProfileIds = "acc_tcga_mutations",
    entrezGeneIds = 1:1000,
    sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01")
)
exps <- molecularData(
    api = cbio,
    molecularProfileIds = c("acc_tcga_rna_seq_v2_mrna", "acc_tcga_rppa"),
    entrezGeneIds = 1:1000,
    sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01")
)

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

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

genePanels(api = cbio)

getGenePanel(api = cbio, genePanelId = "IMPACT341")

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

clinicalData(cbio, "acc_tcga")


getDataByGenes(
    cbio, studyId = "acc_tcga", genes = 1:3,
    by = c("entrezGeneId", "hugoGeneSymbol"),
    molecularProfileIds = "acc_tcga_rppa",
    sampleListId = "acc_tcga_rppa"
)

waldronlab/MultiAssayExperimentData documentation built on Nov. 2, 2024, 3:19 a.m.