## ----lkt---------------------------------------------------------------------- suppressPackageStartupMessages({ library(DT) library(ontoProc) library(magrittr) library(dplyr) library(BiocOncoTK) library(AnnotationHub) 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))