.get_data_by_study {cbioportalR} | R Documentation |
Internal Function to Get Mutations/CNA/Fusion By Study ID
Description
Endpoints for retrieving mutation and cna data are structurally similar.
This internal function allows you to pull data from either endpoint. It has
logic for sensible default guesses at study_id
and molecular_profile_id
when those are NULL
Usage
.get_data_by_study(
study_id = NULL,
molecular_profile_id = NULL,
data_type = c("mutation", "cna", "fusion", "structural_variant", "segment"),
base_url = NULL,
add_hugo = TRUE
)
Arguments
study_id |
A study ID to query mutations. If NULL, guesses study ID based on molecular_profile_id. |
molecular_profile_id |
a molecular profile to query mutations. If NULL, guesses molecular_profile_id based on study ID. |
data_type |
specify what type of data to return. Options are |
base_url |
The database URL to query
If |
add_hugo |
Logical indicating whether |
Value
a dataframe of mutations, CNAs or structural variants
Examples
## Not run:
set_cbioportal_db("public")
.get_data_by_study(study_id = "prad_msk_2019", data_type = "cna")
.get_data_by_study(study_id = "prad_msk_2019", data_type = "mutation")
.get_data_by_study(study_id = "prad_msk_2019", data_type = "fusion")
.get_data_by_study(molecular_profile_id = "prad_msk_2019_cna", data_type = "cna")
.get_data_by_study(molecular_profile_id = "prad_msk_2019_mutations", data_type = "mutation")
.get_data_by_study(molecular_profile_id = "prad_msk_2019_structural_variants", data_type = "fusion")
## End(Not run)