Get clinical data by attribute, study ID and sample ID

Usage

get_clinical_by_sample(
  study_id = NULL,
  sample_id = NULL,
  sample_study_pairs = NULL,
  clinical_attribute = NULL,
  base_url = NULL
)

Arguments

study_id: A string indicating the study ID from which to pull data. If no study ID, will guess the study ID based on your URL and inform. Only 1 study ID can be passed. If mutations/cna from more than 1 study needed, see sample_study_pairs
sample_id: a vector of sample IDs (character)
sample_study_pairs: A dataframe with columns: sample_id, study_id and molecular_profile_id (optional). Variations in capitalization of column names are accepted. This can be used in place of sample_id, study_id, molecular_profile_id arguments above if you need to pull samples from several different studies at once. If passed this will take overwrite sample_id, study_id, molecular_profile_id if also passed.
clinical_attribute: one or more clinical attributes for your study. If none provided, will return all attributes available for studies
base_url: The database URL to query If NULL will default to URL set with set_cbioportal_db(<your_db>)

Value

a dataframe of a specific clinical attribute

Examples

# \dontrun{
get_clinical_by_sample(study_id = "acc_tcga", sample_id = "TCGA-OR-A5J2-01",
 clinical_attribute = "CANCER_TYPE", base_url = 'www.cbioportal.org/api')
#> # A tibble: 1 × 7
#>   uniqueSampleKey                  uniquePatientKey   sampleId patientId studyId
#>   <chr>                            <chr>              <chr>    <chr>     <chr>  
#> 1 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUoyO… TCGA-OR… TCGA-OR-… acc_tc…
#> # ℹ 2 more variables: clinicalAttributeId <chr>, value <chr>

ex <- tibble::tribble(
~sample_id, ~study_id,
"P-0001453-T01-IM3", "blca_nmibc_2017",
"P-0002166-T01-IM3", "blca_nmibc_2017",
"P-0003238-T01-IM5", "blca_nmibc_2017",
"P-0000004-T01-IM3", "msk_impact_2017",
"P-0000023-T01-IM3", "msk_impact_2017")

x <- get_clinical_by_sample(sample_study_pairs = ex,
 clinical_attribute = NULL, base_url = 'www.cbioportal.org/api')
#> ! No `clinical_attribute` passed. Defaulting to returning
#> all clinical attributes in "blca_nmibc_2017" study
#> ! No `clinical_attribute` passed. Defaulting to returning
#> all clinical attributes in "msk_impact_2017" study
 # }