R/prune_byDistance.R

In n-mounier/bGWAS: Bayesian Genome-Wide Association Study

###### Function to distance-prune SNPs ######



# #' Prune set of SNPs
# NOT EXPORTED



prune_byDistance <- function(data, prune.dist=100, byP=T) {
  # data should be : 1st column rs / 2nd column chr / 3rd column pos / 4th column stat
  # if byP = T : stat = p-value -> min is better
  # if byP = F : stat = Zstat, beta.. -> max is better

     if(byP){
       SNP_order = order(data %>% pull(4))
     } else {
       SNP_order = order(data %>% pull(4), decreasing = T)
     }
     data = data[SNP_order,]
     snp=0
     while(T){
       snp=snp+1
       ToRemove=which(data$chr_name==data$chr_name[snp] & abs(data$chr_start - data$chr_start[snp])<prune.dist*1000)
       if(length(ToRemove)>1){
         ToRemove = ToRemove[-1]
         data = data[-ToRemove,]
       }
       if(snp==nrow(data)) break
     }

     return(unlist(data[,1]))

}