dot-get_clinical_by_list_item: Get clinical data by attribute, study ID and sample ID

In cbioportalR: Browse and Query Clinical and Genomic Data from cBioPortal

Get clinical data by attribute, study ID and sample ID

Description

Get clinical data by attribute, study ID and sample ID

Usage

.get_clinical_by_list_item(
  study_id = NULL,
  sample_id = 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)
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

## Not run: 
.get_clinical_by_list_item(study_id = "acc_tcga", sample_id = "TCGA-OR-A5J2-01",
 clinical_attribute = "CANCER_TYPE", base_url = 'www.cbioportal.org/api')
 
## End(Not run)

cbioportalR documentation built on Oct. 6, 2023, 1:07 a.m.