mskcc.oncotree (version 0.1.1)

read_ontology_mappings: Reads ontology_mappings.txt from OncoTree's GitHub repository

Description

Reads `ontology_mappings.txt` from OncoTree's GitHub repository and returns its contents as a tibble.

Usage

read_ontology_mappings(
  url = ontology_mapping_url(),
  fix_names = TRUE,
  list_columns = TRUE
)

Value

A [tibble][tibble::tibble-package] of six variables:

`oncotree_code`

OncoTree code.

`nci_code`

National Cancer Institute (NCI) Thesaurus code.

`umls_code`

Unified Medical Language System (UMLS) code.

`icdo_topography_code`

ICD-O topography code.

`icdo_morphology_code`

ICD-O morphology code.

`hemeonc_code`

HemeOnc code.

Arguments

url

URL of `ontology_mappings.txt`.

fix_names

Whether to convert column names to lowercase, snakecase.

list_columns

Whether to return multi-value variables as list-columns.

Examples

if (FALSE) {
# Import ontology_mappings.txt as tibble
read_ontology_mappings()

# Do not convert column names, i.e. keep them as originally in the file
read_ontology_mappings(fix_names = FALSE)

# Keep multi-value columns as originally, i.e. as comma-separated values
read_ontology_mappings(list_columns = FALSE)
}