Pulls all available sample IDs for a given study ID or sample list ID.
Either a study ID or sample list ID must be passed. If both sample_list and study_id are not NULL,
sample_list ID will be searched and study_id will be ignored.
Arguments
- study_id
A character string indicating which study ID should be searched. Only 1 study ID allowed.
- sample_list_id
A character string indicating which sample list ID should be searched. Only 1 sample list ID allowed.
- base_url
The database URL to query If
NULLwill default to URL set withset_cbioportal_db(<your_db>)
Examples
# \dontrun{
set_cbioportal_db("public")
#> ✔ You are successfully connected!
#> ✔ base_url for this R session is now set to "www.cbioportal.org/api"
available_samples(study_id = "acc_tcga")
#> # A tibble: 92 × 4
#> patientId sampleId sampleType studyId
#> <chr> <chr> <chr> <chr>
#> 1 TCGA-OR-A5J1 TCGA-OR-A5J1-01 Primary Solid Tumor acc_tcga
#> 2 TCGA-OR-A5J2 TCGA-OR-A5J2-01 Primary Solid Tumor acc_tcga
#> 3 TCGA-OR-A5J3 TCGA-OR-A5J3-01 Primary Solid Tumor acc_tcga
#> 4 TCGA-OR-A5J4 TCGA-OR-A5J4-01 Primary Solid Tumor acc_tcga
#> 5 TCGA-OR-A5J5 TCGA-OR-A5J5-01 Primary Solid Tumor acc_tcga
#> 6 TCGA-OR-A5J6 TCGA-OR-A5J6-01 Primary Solid Tumor acc_tcga
#> 7 TCGA-OR-A5J7 TCGA-OR-A5J7-01 Primary Solid Tumor acc_tcga
#> 8 TCGA-OR-A5J8 TCGA-OR-A5J8-01 Primary Solid Tumor acc_tcga
#> 9 TCGA-OR-A5J9 TCGA-OR-A5J9-01 Primary Solid Tumor acc_tcga
#> 10 TCGA-OR-A5JA TCGA-OR-A5JA-01 Primary Solid Tumor acc_tcga
#> # ℹ 82 more rows
available_samples(sample_list_id = "acc_tcga_cna")
#> # A tibble: 90 × 2
#> sampleId sampleListId
#> <chr> <chr>
#> 1 TCGA-OR-A5J1-01 acc_tcga_cna
#> 2 TCGA-OR-A5J2-01 acc_tcga_cna
#> 3 TCGA-OR-A5J3-01 acc_tcga_cna
#> 4 TCGA-OR-A5J4-01 acc_tcga_cna
#> 5 TCGA-OR-A5J5-01 acc_tcga_cna
#> 6 TCGA-OR-A5J6-01 acc_tcga_cna
#> 7 TCGA-OR-A5J7-01 acc_tcga_cna
#> 8 TCGA-OR-A5J8-01 acc_tcga_cna
#> 9 TCGA-OR-A5J9-01 acc_tcga_cna
#> 10 TCGA-OR-A5JA-01 acc_tcga_cna
#> # ℹ 80 more rows
# }