In vjcitn/BiocOncoTK: Bioconductor components for general cancer genomics

Introduction

The TCGA tumor types cover a collection of anatomical compartments. Organizing tumor types into groups of related compartments may be fruitful. We will use the oncotree OBO representation from an NCI thesaurus OBO distribution in the Bioc 3.9 version of ontoProc.

A table

This table was constructed by hand on Oct 10 2019 using materials in ontoProc package.

suppressPackageStartupMessages({
library(DT)
library(ontoProc)
library(magrittr)
library(dplyr)
library(BiocOncoTK)
otree = getOncotreeOnto()
})
data("map_tcga_ncit")
datatable(map_tcga_ncit)

Formal annotation of anatomic site

Expeditious mapping

We will drop the CNTL class, and use only the first NCIT mapping when two seem to match.

controlindex = which(map_tcga_ncit[,1]=="CNTL")
tcgacodes = map_tcga_ncit[-controlindex,1]
ncitsites = map_tcga_ncit[-controlindex,3]
ssi = strsplit(ncitsites, "\\|")
sites = sapply(ssi, "[", 1)
simpmap = data.frame(code=tcgacodes, oncotr_site=otree$name[sites], ncit=sites,
  stringsAsFactors=FALSE)
simpmap[sample(seq_len(nrow(simpmap)),5),]

We now have a 1-1 mapping from TCGA code to NCIT site. These sites can be grouped according to organ system, using the knowledge that NCIT:C3263 is the 'neoplasm by site' (which really should be 'system') category.

poss_sys = otree$children["NCIT:C3263"][[1]] # all possible systems
allanc = otree$ancestors[simpmap$ncit]
specific = sapply(allanc, function(x) intersect(x, poss_sys)[1]) # ignore multiplicities
sys = unlist(otree$name[specific])
datatable(systab <- cbind(simpmap, sys=sys))

Neither thymoma nor mesothelioma have NCIT organ system mappings per se.

Aggregation

We now have 12 categories for 33 tumor types. A code pattern for finding the TCGA codes for a given system is:

systab %>% filter(grepl("Repro", sys))

vjcitn/BiocOncoTK documentation built on Feb. 14, 2023, 11:56 p.m.