mskcc.oncotree (version 0.1.1)

umls_to_oncotree: Map UMLS to OncoTree codes

Description

This function maps Unified Medical Language System (UMLS) codes to OncoTree codes.

Usage

umls_to_oncotree(
  umls_code = NULL,
  oncotree_version = "oncotree_latest_stable",
  expand = FALSE
)

Value

A tibble of two variables: umls_code and oncotree_code.

Arguments

umls_code

UMLS codes.

oncotree_version

OncoTree database release version.

expand

Whether to expand one-to-many mappings. If TRUE, one-to-many mappings are expanded into several rows in the output.

Examples

if (FALSE) {
# Leave `umls_code` empty to return mappings for all UMLS codes
umls_to_oncotree()

# Map a few selected OncoTree codes
umls_to_oncotree(umls_code = c('C0206642', 'C0600113', 'C0279654', 'C1707436'))

# Use `expand` to make sure the column `oncotree_code` is a character vector and
# not a list-column. One-to-many mappings will result in more than row with
# `oncotree_code` values repeated.
umls_to_oncotree(umls_code = c('C0206642', 'C0600113', 'C0279654', 'C1707436'), expand = TRUE)
}