cbioportalR (version 1.1.0)

get_clinical_by_sample: 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_sample(
  study_id = NULL,
  sample_id = NULL,
  sample_study_pairs = 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)

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>)

Examples

if (FALSE) {
get_clinical_by_sample(study_id = "acc_tcga", sample_id = "TCGA-OR-A5J2-01",
 clinical_attribute = "CANCER_TYPE", base_url = 'www.cbioportal.org/api')

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')
 }