get_genetics_by_study {cbioportalR}

Get All Genomic Information By Study

Description

Get All Genomic Information By Study

Usage

get_genetics_by_study(
  study_id = NULL,
  add_hugo = TRUE,
  base_url = NULL,
  return_segments = FALSE
)

Arguments

study_id

A study ID to query mutations. If NULL, guesses study ID based on molecular_profile_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>)⁠

return_segments

Default is FALSE where copy number segmentation data won't be returned in addition to the mutation, cna and structural variant data. TRUE will return any available segmentation data with results.

Value

A list of mutations, cna and structural variants (including fusions), if available. Will also return copy number segmentation data if return_segments = TRUE.

Examples

## Not run: 
get_genetics_by_study(study_id = "prad_msk_2019")

## End(Not run)