cbioportalR (version 1.1.0)

.get_clinical_by_list_item: 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
)

Value

a dataframe of a specific clinical attribute

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>)

Examples

if (FALSE) {
.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')
 }