In bhklab/AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data

knitr::opts_chunk$set(
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Introduction

OncoTree is a standardized classification system used in cancer research and clinical practice to categorize different types of cancer based on their tissue of origin, molecular characteristics, and other relevant factors. Developed by the National Cancer Institute (NCI) within the United States, OncoTree provides a hierarchical framework that organizes cancer types into a structured tree-like diagram.

• provides a standardized classification system for categorizing different types of cancer based on their tissue of origin, molecular characteristics, and other relevant factors.
• provides a hierarchical framework that organizes cancer types into a structured tree-like diagram.
• useful for ensuring consistency in how cancer types are classified and reported across different studies and clinical settings.

Setup

library(AnnotationGx)

Querying OncoTree

AnnotationGx provides a set of functions for querying OncoTree to retrieve three types of information: - OncoTree release versions - Main Cancer types - Subtypes of a specific cancer type and their relationships

OncoTree release versions

The getOncotreeVersions function retrieves the available OncoTree release.

getOncotreeVersions()

Main Cancer types

The getMainCancerTypes function retrieves the main cancer types in OncoTree.

getOncotreeMainTypes()

Subtypes of a specific cancer type

The getCancerSubtypes function retrieves the subtypes of a specific cancer type.

getOncotreeTumorTypes()

bhklab/AnnotationGx documentation built on April 3, 2025, 4:27 p.m.