get_mutations_by_study: Get Mutations By Study ID

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

Get Mutations By Study ID

Description

Get Mutations By Study ID

Usage

get_mutations_by_study(
  study_id = NULL,
  molecular_profile_id = NULL,
  add_hugo = TRUE,
  base_url = NULL
)

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.
add_hugo	Logical indicating whether HugoGeneSymbol should be added to your resulting data frame, if not already present in raw API results. Argument is TRUE by default. If FALSE, results will be returned as is (i.e. any existing Hugo Symbol columns in raw results will not be removed).
base_url	The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

A dataframe of mutations (maf file format)

Examples

## Not run: 
get_mutations_by_study(study_id = "prad_msk_2019")
get_mutations_by_study(molecular_profile_id = "prad_msk_2019_mutations")

## End(Not run)

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