umls_to_oncotree: Map UMLS to OncoTree codes

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

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
)

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.

Value

A tibble of two variables: umls_code and oncotree_code.

Examples

## Not run: 
# 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)

## End(Not run)

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