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 )#> # A tibble: 92 x 7 #> uniqueSampleKey uniquePatientKey molecularProfil… sampleId patientId studyId #> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 VENHQS1PUi1BNUo… VENHQS1PUi1BNUo… acc_tcga_linear… TCGA-OR… TCGA-OR-… acc_tc… #> 2 VENHQS1PUi1BNUo… VENHQS1PUi1BNUo… acc_tcga_linear… TCGA-OR… TCGA-OR-… acc_tc… #> 3 VENHQS1PUi1BNUo… VENHQS1PUi1BNUo… acc_tcga_linear… TCGA-OR… TCGA-OR-… acc_tc… #> 4 VENHQS1PUi1BNUo… VENHQS1PUi1BNUo… acc_tcga_linear… TCGA-OR… TCGA-OR-… acc_tc… #> 5 VENHQS1PUi1BNUo… VENHQS1PUi1BNUo… acc_tcga_linear… TCGA-OR… TCGA-OR-… acc_tc… #> 6 VENHQS1PUi1BNUo… VENHQS1PUi1BNUo… acc_tcga_linear… TCGA-OR… TCGA-OR-… acc_tc… #> 7 VENHQS1PUi1BNUp… VENHQS1PUi1BNUp… acc_tcga_linear… TCGA-OR… TCGA-OR-… acc_tc… #> 8 VENHQS1PUi1BNUp… VENHQS1PUi1BNUp… acc_tcga_linear… TCGA-OR… TCGA-OR-… acc_tc… #> 9 VENHQS1PUi1BNUp… VENHQS1PUi1BNUp… acc_tcga_linear… TCGA-OR… TCGA-OR-… acc_tc… #> 10 VENHQS1PUi1BNUp… VENHQS1PUi1BNUp… acc_tcga_linear… TCGA-OR… TCGA-OR-… acc_tc… #> # … with 82 more rows, and 1 more variable: profiled <lgl>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