inst/doc/maptcga.R

In BiocOncoTK: Bioconductor components for general cancer genomics

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

## ----lkanno-------------------------------------------------------------------
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),]

## ----findsys------------------------------------------------------------------
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))

## ----lkca---------------------------------------------------------------------
systab %>% filter(grepl("Repro", sys))