cBioPortalData: Download data from the cBioPortal API

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

Description

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.

Usage

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

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.

Value

A MultiAssayExperiment object

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
)

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

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