combine_imprinted_genes.R

   1 library(data.table)
   2
   3 args <- commandArgs(trailingOnly=TRUE)
   4
   5 geneimprint <- fread(args[1])
   6 geneimprint <- geneimprint[!grepl(" ",Gene),]
   7
   8 geneimprint <- geneimprint[Status!="Not Imprinted",]
   9 geneimprint <- geneimprint[Status!="Unknown",]
  10
  11 parent <- fread(args[2])
  12 ### fix up the 0 prefixed chromosomes
  13 parent[,chr:=gsub("^0","",chromosome)]
  14 ### remove aliases in ()
  15 parent[,Gene:=gsub("\\s*\\([^\\)]+\\)\\s*","",gene)]
  16 ### remove aliases after ,
  17 parent[,Gene:=gsub("\\s*,\\s*.+","",Gene)]
  18
  19 parent <- parent[grepl("^[A-Z0-9]+$",Gene),]
  20
  21
  22 setkey(parent,"Gene")
  23 setkey(geneimprint,"Gene")
  24
  25 imprinted.genes <-
  26     union(gsub("[\\*\\@]$","",parent[,Gene]),
  27           gsub("[\\*\\@]$","",geneimprint[,Gene]))
  28
  29 gene.aliases <- fread(args[3])
  30 setkey(gene.aliases,"alias")
  31
  32 imprinted.genes <-
  33     sort(sapply(imprinted.genes,
  34            function(x){if(is.na(gene.aliases[x,gene])) {
  35                            return(x)
  36                        } else {
  37                            return(gene.aliases[x,gene])
  38                        }}))
  39
  40 write.table(file=args[length(args)],
  41             imprinted.genes,
  42             sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
  43