R/d4_mfac.R

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

#' Function to obtain the AUPR and AUROC in the DREAM4 Multifactorial Challenge.
#' @param g a number larger than 0, width parameter for the RBF Kernel
#' @param v a number between 0 and 1 that is the shrinkage parameter
#' @param ite an integer with number of iterations.
#' @param write_res a logical to indicate if the tables should be written.
#' @export
#' @return list with auroc and auprs of the DREAM4 multifactorial challenge.
#' @examples
#' res = d4_mfac()
#'
d4_mfac <- function(v,g,ite, write_res){
    # Pre-allocate memory for the results.
    aurocs <- matrix(0,5,1)
    auprs <- matrix(0,5,1)
    # Run the data.
    grn_1 <- kboost(KBoost::D4_multi_1,v = v,g = g, ite= ite)
    grn_2 <- kboost(KBoost::D4_multi_2,v = v,g = g, ite= ite)
    grn_3 <- kboost(KBoost::D4_multi_3,v = v,g = g, ite= ite)
    grn_4 <- kboost(KBoost::D4_multi_4,v = v,g = g, ite= ite)
    grn_5 <- kboost(KBoost::D4_multi_5,v = v,g = g, ite= ite)
    # Now format the gold standards.
    g_mat1 <- tab_2_matrix_D4(KBoost::G_D4_multi_1,100)
    g_mat2 <- tab_2_matrix_D4(KBoost::G_D4_multi_2,100)
    g_mat3 <- tab_2_matrix_D4(KBoost::G_D4_multi_3,100)
    g_mat4 <- tab_2_matrix_D4(KBoost::G_D4_multi_4,100)
    g_mat5 <- tab_2_matrix_D4(KBoost::G_D4_multi_5,100)
    # Now obtain the AUROCS and the AUPRS.
    a <- AUPR_AUROC_matrix(grn_1$GRN,g_mat1,TRUE,seq_len(100))
    aurocs[1] <- a$AUROC
    auprs[1] <- a$AUPR
    a <- AUPR_AUROC_matrix(grn_2$GRN,g_mat2,TRUE,seq_len(100))
    aurocs[2] <- a$AUROC
    auprs[2] <- a$AUPR
    a <- AUPR_AUROC_matrix(grn_3$GRN,g_mat3,TRUE,seq_len(100))
    aurocs[3] <- a$AUROC
    auprs[3] <- a$AUPR
    a <- AUPR_AUROC_matrix(grn_4$GRN,g_mat4,TRUE,seq_len(100))
    aurocs[4] <- a$AUROC
    auprs[4] <- a$AUPR
    a <- AUPR_AUROC_matrix(grn_5$GRN,g_mat5,TRUE,seq_len(100))
    aurocs[5] <- a$AUROC
    auprs[5] <- a$AUPR
    if (missing(write_res)){
        write_res <- FALSE
    }
    if (write_res){
        file_ <- "KBoost_D4_"
        write_GRN_D4(grn_1$GRN,TFs = seq_len(100), filename= paste(file_, "_1.txt", sep = ""))
        write_GRN_D4(grn_2$GRN,TFs =  seq_len(100), filename =paste(file_, "_2.txt", sep = ""))
        write_GRN_D4(grn_3$GRN,TFs =  seq_len(100), filename = paste(file_, "_3.txt", sep = ""))
        write_GRN_D4(grn_4$GRN,TFs =  seq_len(100), filename =paste(file_, "_4.txt", sep = ""))
        write_GRN_D4(grn_5$GRN,TFs =  seq_len(100), filename =  paste(file_, "_5.txt", sep = ""))
    }
    return(list(aurocs = aurocs, auprs= auprs))
}