cBioPortal: The R interface to the cBioPortal API Data Service

In cBioPortalData: Exposes and makes available data from the cBioPortal web resources

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/api-docs"
)

getStudies(api)

clinicalData(api, studyId = NA_character_)

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

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

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

searchOps(api, keyword)

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

samplesInSampleLists(api, sampleListIds = NA_character_)

sampleLists(api, studyId = NA_character_)

allSamples(api, studyId = NA_character_)

genePanels(api)

getGenePanel(api, genePanelId = NA_character_)

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

getGenePanelMolecular(api, molecularProfileIds = NA_character_, sampleIds)

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

getDataByGenePanel(
  api,
  studyId = NA_character_,
  genePanelId = NA_character_,
  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/api-docs')
api	An API object of class 'cBioPortal' from the 'cBioPortal' function
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
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
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()“

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

* searchOps - Search through API operations with a keyword

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

* sampleLists - obtain all 'sampleListIds' for a particular 'studyId'

* allSamples - obtain all samples within a particular 'studyId'

* genePanels - Show all available gene panels

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')

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

Mutation Data

* mutationData - Produce a dataset of mutation data using '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 paricular 'molecularProfileId' and 'sampleListId' combination

* getGenePanelMolecular - get gene panel data for a combination of 'molecularProfileId' and 'sampleListId' vectors

* getDataByGenePanel - Download data for a gene panel and 'molecularProfileId' combination, 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")


getDataByGenePanel(cbio, studyId = "acc_tcga", genePanelId = "IMPACT341",
   molecularProfileId = "acc_tcga_rppa", sampleListId = "acc_tcga_rppa")

cBioPortalData documentation built on April 17, 2021, 6:07 p.m.