read_ontology_mappings {mskcc.oncotree} | R Documentation |
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)
[Package mskcc.oncotree version 0.1.1 Index]