R/write_GRN_D4.R

In Luisiglm/KBoost: Inference of gene regulatory networks from gene expression data

#' Function to write output in DREAM4 Challenge Format.
#' @param GRN a GxK gene regulatory network.
#' @param TFs a K set of indixes of G that are TFs.
#' @param filename a string with the filename.
#' @export
#' @return a file with the network written as a file.
#' @examples
#' data(D4_multi_1)
#' Net = kboost(D4_multi_1)
#' write_GRN_D4(Net$GRN, seq_len(100), "D4_multi_1_network.txt")
write_GRN_D4 <- function(GRN,TFs, filename){
    G <- dim(GRN)[1]
    K <- dim(GRN)[2]
    # if no colnames and rownames are set.
    # Table form results.
    table_grn <- matrix("i",G*K-K,3)
    table_no <- matrix(0,G*K-K,1)
    if (is.null(rownames(GRN))){
        # Create generic names.
        gen_names <- matrix("G",G,1)
        for (i in seq_len(G)){
            gen_names[i] <- paste(gen_names[i],toString(i),sep = "")
        }
    } else {
        gen_names <- rownames(GRN)
    }
    # start counter
    count_ <- 1
    for (j in seq_len(K)){
        for (i in seq_len(G)){
            # write in table.
            if (TFs[j]!=i){
                table_grn[count_, ] <- c(gen_names[TFs[j]], gen_names[i] , toString(GRN[i,j]))
                table_no[count_] <- GRN[i,j]
                count_ <- count_  +1
            }
        }
    }
    o <- order(table_no, decreasing = TRUE)
    utils::write.table(table_grn[o,], filename, col.names = FALSE, row.names = FALSE, quote = FALSE)  
}