R/stratSampling.R

In takahirosuzuki1980/InfiniumDiffMetMotR: Motif Overrepresentation analysis for Illumina Methylation Arrays

#' Stratified sampling
#' 
#' stratified sampling of same number of target probes based on annotation categolies of target probes(TSS200, CGI, CpG shore, CpG shelf, and other region)
#' 
#' @param target_IDs methylation array IDs of DMP
#' @param anno_info annotation infromation of probe
#' 
#' @importFrom stats runif
#' 
#' @return probe IDs
#' 
#' @keywords stratified sampling, random
#' @export

stratSampling <- function(target_IDs, anno_info=InfiniumDiffMetMotR::EPICanno){
 ##Categolization of all probes into the categolies
  all.TSS.probes <- as.vector(anno_info[unique(c(grep("TSS200", anno_info[,"UCSC_RefGene_Group"]), grep("5'UTR", anno_info[,"UCSC_RefGene_Group"]))),"IlmnID"])    #identification of all TSS probes
  all.nonTSS <- anno_info[!(anno_info[,"IlmnID"] %in% all.TSS.probes),]
  all.CGI.probes <- as.vector(all.nonTSS[grep("Island", all.nonTSS[,"Relation_to_UCSC_CpG_Island"]),"IlmnID"])    #identification of all CGI probes
  all.shore.probes <- as.vector(all.nonTSS[grep("Shore", all.nonTSS[,"Relation_to_UCSC_CpG_Island"]),"IlmnID"])    #identification of all shore probes
  all.shelf.probes <- as.vector(all.nonTSS[grep("Shelf", all.nonTSS[,"Relation_to_UCSC_CpG_Island"]),"IlmnID"])    #identification of all shelf probes
  all.other.probes <- setdiff(setdiff(setdiff(setdiff(anno_info[,"IlmnID"],all.TSS.probes), all.CGI.probes), all.shore.probes),all.shelf.probes)    #identification of all non-TSS, non-CGI, non-shore probes

  ##number of probes in each categolies
  nall.TSS.probes <- length(all.TSS.probes)    #number of all CGI probes
  nall.CGI.probes <- length(all.CGI.probes)    #number of all CGI probes
  nall.shore.probes <- length(all.shore.probes)    #number of all shore probes
  nall.shelf.probes <- length(all.shelf.probes)    #number of all shelf probes
  nall.other.probes <- length (all.other.probes)    #number of all non-CGI/non-shore/probes


  ## identification of DMPs in each categolies (TSS, CpG Island, CpG Shore, others)
  TSS.probes <- target_IDs[target_IDs %in% all.TSS.probes]    #identification of TSS DMPs
  CGI.probes <- target_IDs[target_IDs %in% all.CGI.probes]    #identification of CGI DMPs within non-TSS probes
  shore.probes <- target_IDs[target_IDs %in% all.shore.probes]    #identification of shore DMPs within non-TSS probes
  shelf.probes <- target_IDs[target_IDs %in% all.shelf.probes]    #identification of shelf DMPs within non-TSS probes
  other.probes <- target_IDs[target_IDs %in% all.other.probes]    #identification of non-TSS, non-CGI, non-shore probes

  ## number of DMPs in each categilies
  nTSS.probes <- length(TSS.probes)    #number of CGI DMPs
  nCGI.probes <- length(CGI.probes)    #number of CGI DMPs
  nshore.probes <- length(shore.probes)    #number of shore DMPs
  nshelf.probes <- length(shelf.probes)    #number of shore DMPs
  nnonCGI.probes <- length(other.probes)    #number of non-CGI/non-shore DMPs

  ##ramdom sampling from each categolies
  set.seed(123)
  ran.TSS.probes <- all.TSS.probes[floor(runif(nTSS.probes, 1, nall.TSS.probes))]    #TSS probes
  ran.CGI.probes <- all.CGI.probes[floor(runif(nCGI.probes, 1 ,nall.CGI.probes))]    #CGI probes
  ran.shore.probes <- all.shore.probes[floor(runif(nshore.probes, 1 ,nall.shore.probes))]    #shore probes
  ran.shelf.probes <- all.shore.probes[floor(runif(nshelf.probes, 1 ,nall.shelf.probes))]    #shelf probes
  ran.other.probes <- all.other.probes[floor(runif(nnonCGI.probes, 1 ,nall.other.probes))]    #other probes
  ran.probes <- c(ran.TSS.probes, ran.CGI.probes, ran.shore.probes, ran.shelf.probes, ran.other.probes)
  set.seed(NULL)
  return (ran.probes)
}