Get tumor types — get_tumor_types • mskcc.oncotree

Get tumor types according to OncoTree's ontology.

Usage

get_tumor_types(oncotree_version = "oncotree_latest_stable")

oncotree_version: OncoTree version. Check available options with get_versions().

A tibble of 13 variables:

oncotree_version: OncoTree tumor classification system version.
oncotree_code: Tumor type code: a unique identifier for a tumor type within the classification system of the OncoTree.
oncotree_name: Tumor type name: a brief description of the tumor type.
oncotree_main_type: Tumor main type: a category under which the tumor type can be grouped.
tissue: Tissue associated with the tumor type.
level: OncoTree is a hierachical classification system with 5 levels. At the root level (level 0) there is the single "TISSUE" tumor type. At level 1, there are 32 tissue sites, e.g., "BREAST".
parent: The parent is the parent oncotree_code for this tumor type.
umls_code: The corresponding tumor type identifier(s) in the Unified Medical Language System (UMLS).
nci_code: The corresponding tumor type identifier(s) in the National Cancer Institute (NCI) Thesaurus.
history: Previous tumor type codes (from previous OncoTree versions) used to identify this tumor type.
revocations: TODO.
precursors: TODO.
color: Color associated with the tumor type.

if (FALSE) {
get_tumor_types()
}