Download data from the cBioPortal API

Source: R/cBioPortalData.R

Obtain a MultiAssayExperiment object for a particular gene panel, studyId, molecularProfileIds, and sampleListIds combination. Default molecularProfileIds and sampleListIds are set to NULL for including all data. This option is best for users who wish to obtain a section of the study data that pertains to a specific molecular profile and gene panel combination. For users looking to download the entire study data as provided by the https://cbioportal.org/datasets, refer to cBioDataPack.

cBioPortalData(
  api,
  studyId = NA_character_,
  genePanelId = NA_character_,
  molecularProfileIds = NULL,
  sampleListId = NULL,
  by = c("entrezGeneId", "hugoGeneSymbol")
)

Arguments

api

An API object of class `cBioPortal` from the `cBioPortal` function
studyId

character(1) Indicates the "studyId" as taken from `getStudies`
genePanelId

character(1) Identifies the gene panel, as obtained from the `genePanels` function
molecularProfileIds

character() A vector of molecular profile IDs
sampleListId

character(1) A sample list identifier as obtained from `sampleLists()``
by

character(1) Either 'entrezGeneId' or 'hugoGeneSymbol' for row metadata

Value

A MultiAssayExperiment object

Details

As of May 2020, there were about 96.6 percent of the 268 datasets successfully imported. The datasets that currently fail to import are:

        c("all_stjude_2015", "sclc_ucologne_2015", "skcm_ucla_201
        "sclc_jhu", "gbm_tcga_pub2013", "hnsc_tcga_pub", "kirc_tc
        "brca_tcga_pub", "brca_tcga_pub2015")

Note that changes to the cBioPortal API may affect this rate at any time. If you encounter any issues, please open a GitHub issue at the https://github.com/waldronlab/cBioPortalData/issues/ page with a fully reproducible example.

See also

cBioDataPack

Examples


cbio <- cBioPortal()

samps <- samplesInSampleLists(cbio, "acc_tcga_rppa")[[1]]

getGenePanelMolecular(
    cbio, molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA"),
    samps
)

#> Error in gsub(finish, start, ..., fixed = TRUE): zero-length pattern

acc_tcga <- cBioPortalData(
    cbio, by = "hugoGeneSymbol",
    studyId = "acc_tcga",
    genePanelId = "AmpliSeq",
    molecularProfileIds =
        c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations")
)

#> Error in eval(args[["api"]]): object 'cbio' not found