get_clinical_by_study: Get all available clinical data for a specified study

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

Get all available clinical data for a specified study

Description

Returns all sample-level and patient-level clinical data for a given study

Usage

get_clinical_by_study(
  study_id = NULL,
  clinical_attribute = NULL,
  base_url = NULL
)

Arguments

study_id	study ID
clinical_attribute	one or more clinical attributes for your study. If none provided, will return all attributes available for that study (⁠available_clinical_attributes(<study_id>)⁠)
base_url	The database URL to query. If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

a dataframe of all available clinical attributes and their values

Examples

## Not run: 
get_clinical_by_study(study_id = "acc_tcga",
 clinical_attribute = "CANCER_TYPE", base_url = 'www.cbioportal.org/api')

get_clinical_by_study(study_id = "acc_tcga", base_url = 'www.cbioportal.org/api')

## End(Not run)

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