cbioportalR (version 1.1.0)

get_segments_by_sample: Get Copy Number Segmentation Data By Sample ID

Description

Get Copy Number Segmentation Data By Sample ID

Usage

get_segments_by_sample(
  sample_id = NULL,
  study_id = NULL,
  sample_study_pairs = NULL,
  base_url = NULL
)

Value

A dataframe of CNA segments

Arguments

sample_id

a vector of sample IDs (character)

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_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.

base_url

The database URL to query If NULL will default to URL set with set_cbioportal_db(<your_db>)

Examples

if (FALSE) {
set_cbioportal_db("public")

get_segments_by_sample(sample_id = c("s_C_CAUWT7_P001_d"),
                 study_id = "prad_msk_2019")
                 }