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") )
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 |
A MultiAssayExperiment object
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.
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 patternacc_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