R/match_expr_methy.R

In NWPU-903PR/m6AexpressBHM: m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model

##Match gene expression and methylation level for candidate genes
match_expr_methy <- function(gene_express_data,gene_methy){
  gene_express <- gene_express_data$gene_express
  express_sizefactor <- gene_express_data$size_factor
  full_expression <- apply(gene_express,1,sum)
  select_label <- which(full_expression>10)
  full_expr_gene <- gene_express[select_label,]
  target_genes <- intersect(rownames(gene_methy),rownames(full_expr_gene))
  gene_exp_methy <- data.frame()
  for (i in 1:length(target_genes)) {
    one_exp_methy <- c(as.numeric(as.character(full_expr_gene[rownames(full_expr_gene)==target_genes[i],])),
                      as.numeric(as.character(gene_methy[rownames(gene_methy)==target_genes[i],])))
    gene_exp_methy <- rbind(gene_exp_methy,one_exp_methy)
  }
  rownames(gene_exp_methy) <- target_genes
  colnames(gene_exp_methy) <- c(colnames(full_expr_gene),colnames(gene_methy))
  
  gene_expr_methy_infor <- list(gene_expr_methy=gene_exp_methy,
                                library_sizefactor=express_sizefactor)
  return(gene_expr_methy_infor)
}