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_, genes = NA_character_, molecularProfileIds = NULL, sampleListId = NULL, sampleIds = 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 |
| genes | character() Either Entrez gene identifiers or Hugo gene symbols. When included, the 'by' argument indicates the type of identifier provided and 'genePanelId' is ignored. Preference is given to Entrez IDs due to faster query responses. |
| molecularProfileIds | character() A vector of molecular profile IDs |
| sampleListId | character(1) A sample list identifier as obtained from `sampleLists()`` |
| sampleIds | character() Sample identifiers |
| by | character(1) Either 'entrezGeneId' or 'hugoGeneSymbol' for row metadata (default: 'entrezGeneId') |
A MultiAssayExperiment object
We are able to succesfully represent 98 percent of the study
identifiers as MultiAssayExperiment objects as obtained via
cBioPortalData with the IMPACT341 genePanelId as the example
gene panel. Datasets that currently fail to import
can be seen in the getStudies(..., buildReport = TRUE) dataset
under the "api_build" column.
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 × 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