R/peak_sites_filter.R

In NWPU-903PR/m6AexpressReader: Predicting context-specific m6A regulation of gene expression combinding m6A reader binding information

peak_site_filter <- function(m6Asites_infor, num_cond1, filter_reads_num){
  m6Asite_readsinfor <- m6Asites_infor[[1]]
  methy_read <- m6Asite_readsinfor[,grep("IP",colnames(m6Asite_readsinfor))]
  CTL_methy_read <- methy_read[,1:num_cond1]
  Treated_methy_read <- methy_read[,-match(colnames(CTL_methy_read),colnames(methy_read))]
  colnames(CTL_methy_read) <- paste0("untreated_IP",1:ncol(CTL_methy_read))
  colnames(Treated_methy_read) <- paste0("treated_IP",1:ncol(Treated_methy_read))
  ####
  CTL_methy_selectlabel <- which(rowMeans(CTL_methy_read)>filter_reads_num)
  Treated_methy_selectlabel <- which(rowMeans(Treated_methy_read)>filter_reads_num)
  methy_selectlable <- intersect(CTL_methy_selectlabel,Treated_methy_selectlabel)
  ####
  unmethy_read <- m6Asite_readsinfor[,grep("Input", colnames(m6Asite_readsinfor))]
  CTL_unmethy_read <- as.data.frame(unmethy_read[,1:num_cond1])
  Treated_unmethy_read <- unmethy_read[,-(match(colnames(CTL_unmethy_read),colnames(unmethy_read)))]
  colnames(CTL_unmethy_read) <- paste0("untreated_Input",1:ncol(CTL_unmethy_read))
  colnames(Treated_unmethy_read) <- paste0("treated_Input", 1:ncol(Treated_unmethy_read))
  ####
  CTL_unmethy_selectlabel <- which(rowMeans(CTL_unmethy_read)>filter_reads_num)
  Treated_unmethy_selectlabel <- which(rowMeans(Treated_unmethy_read)>filter_reads_num)
  unmethy_selectlable <- intersect(CTL_unmethy_selectlabel,Treated_unmethy_selectlabel)
  ####
  select_label <- intersect(methy_selectlable,unmethy_selectlable)
  
  peak_reads_filter <- m6Asite_readsinfor[select_label,]
  return(peak_reads_filter)
}