ffl: Identifies Feed Forward Gene Networks

#file: DE-method/DEm-3a-arm3a-fn-v1.R

# arm3a: miRNA-TF ---------------------------------------------------------


# arm3a prep --------------------------------------------------------------


# arm3a function ----------------------------------------------------------

###########arm3a_miRNA_tf function
#use miRNA-mRNA correlated pairs output from arm1 (anamir)
#' @title DEm_arm3a_miRNA_tf
#' @description identifies valid miRNA-TF (miRNA regulates TF) pairs for FFL among miRNA-gene pairs
#'
#' @param miRNA_gene_pairs dataframe of miRNA-gene pairs, output from arm1
#'
#' @return dataframe of miRNA-TF pairs that were found in databases
#'
DEm_arm3a_miRNA_tf <- function(miRNA_gene_pairs){
  #from miRNA-gene pairs, keep miRNA-TF pairs
  db_hits <- miRNA_gene_pairs[miRNA_gene_pairs$gene %in% arm2_tf_list, ]
  #rename "gene" in column names to "TF"
  names(db_hits)[names(db_hits) == "gene"] <- "TF"
  names(db_hits)[names(db_hits) == "Ensembl_ID_gene"] <- "Ensembl_ID_TF"
  names(db_hits)[names(db_hits) == "GeneID_gene"] <- "GeneID_TF"
  names(db_hits)[names(db_hits) == "sum_db_hits_miRNAgene"] <- "sum_db_hits_miRNATF"
  print(paste(dim(db_hits)[1], "miRNA-TF pairs found in at least one database", sep = " "))

  return(db_hits)
}