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

In maialab/mskcc.oncotree: Interface to the 'OncoTree' API

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
)

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

## Not run: 
# 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)

## End(Not run)

maialab/mskcc.oncotree documentation built on Oct. 15, 2022, 12:01 p.m.