Reads ontology_mappings.txt from OncoTree's GitHub repository — read_ontology_mappings • mskcc.oncotree

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
)

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.

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.

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)
}