Nothing
# Wrapper function:
SILGGM <- function(x, method = NULL, lambda = NULL, global = FALSE, alpha = NULL, ndelta = NULL, true_graph = NULL, cytoscape_format = FALSE, csv_save = FALSE, directory = NULL){
result <- SILGGMCpp(x, method, lambda, global, alpha, ndelta, true_graph)
if(cytoscape_format == FALSE){
return(result)
}
else{
cytoscape_format_table = list()
if(is.null(method) || method == "D-S_NW_SL"){
pair <- melt(upper.tri(result$precision))
pair <- pair[pair[,3] %in% TRUE,c(1,2)]
row.names(pair) <- NULL
precision <- result$precision[upper.tri(result$precision)]
partialCor <- result$partialCor[upper.tri(result$partialCor)]
CI_low_precision <- result$CI_low_precision[upper.tri(result$CI_low_precision)]
CI_high_precision <- result$CI_high_precision[upper.tri(result$CI_high_precision)]
z_score_precision <- result$z_score_precision[upper.tri(result$z_score_precision)]
p_precision <- result$p_precision[upper.tri(result$p_precision)]
if(global == FALSE){
corr_table <- cbind(pair, precision, partialCor, CI_low_precision, CI_high_precision, z_score_precision, p_precision)
colnames(corr_table) <- c("gene1","gene2","precision","partialCor","CI_low_precision","CI_high_precision","z_score_precision","p_precision")
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_D-S_NW_SL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
else{
if(is.null(true_graph)){
cytoscape_format_table$threshold <- result$threshold
cytoscape_format_table$FDR <- result$FDR
global_decision <- NULL
if(is.null(alpha)){
alpha_length <- 2
}
else{
alpha_length <- length(alpha)
}
for(i in 1:alpha_length){
global_decision1 <- result$global_decision[[i]][upper.tri(result$global_decision[[i]])]
global_decision <- cbind(global_decision, global_decision1)
}
if(is.null(alpha)){
colnames(global_decision) <- c("global_decision_0.05","global_decision_0.1")
}
else{
for(i in 1:alpha_length){
colnames(global_decision)[i] <- paste("global_decision",alpha[i],sep="_")
}
}
corr_table <- cbind(pair, precision, partialCor, CI_low_precision, CI_high_precision, z_score_precision, p_precision, global_decision)
colnames(corr_table) <- c("gene1","gene2","precision","partialCor","CI_low_precision","CI_high_precision","z_score_precision","p_precision",colnames(global_decision))
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_D-S_NW_SL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
else{
cytoscape_format_table$threshold <- result$threshold
cytoscape_format_table$FDR <- result$FDR
cytoscape_format_table$power <- result$power
global_decision <- NULL
if(is.null(alpha)){
alpha_length <- 2
}
else{
alpha_length <- length(alpha)
}
for(i in 1:alpha_length){
global_decision1 <- result$global_decision[[i]][upper.tri(result$global_decision[[i]])]
global_decision <- cbind(global_decision, global_decision1)
}
if(is.null(alpha)){
colnames(global_decision) <- c("global_decision_0.05","global_decision_0.1")
}
else{
for(i in 1:alpha_length){
colnames(global_decision)[i] <- paste("global_decision",alpha[i],sep="_")
}
}
corr_table <- cbind(pair, precision, partialCor, CI_low_precision, CI_high_precision, z_score_precision, p_precision, global_decision)
colnames(corr_table) <- c("gene1","gene2","precision","partialCor","CI_low_precision","CI_high_precision","z_score_precision","p_precision",colnames(global_decision))
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_D-S_NW_SL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
}
}
if(method == "D-S_GL"){
pair <- melt(upper.tri(result$precision))
pair <- pair[pair[,3] %in% TRUE,c(1,2)]
row.names(pair) <- NULL
precision <- result$precision[upper.tri(result$precision)]
partialCor <- result$partialCor[upper.tri(result$partialCor)]
CI_low_precision <- result$CI_low_precision[upper.tri(result$CI_low_precision)]
CI_high_precision <- result$CI_high_precision[upper.tri(result$CI_high_precision)]
z_score_precision <- result$z_score_precision[upper.tri(result$z_score_precision)]
p_precision <- result$p_precision[upper.tri(result$p_precision)]
if(global == FALSE){
corr_table <- cbind(pair, precision, partialCor, CI_low_precision, CI_high_precision, z_score_precision, p_precision)
colnames(corr_table) <- c("gene1","gene2","precision","partialCor","CI_low_precision","CI_high_precision","z_score_precision","p_precision")
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_D-S_GL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
else{
if(is.null(true_graph)){
cytoscape_format_table$threshold <- result$threshold
cytoscape_format_table$FDR <- result$FDR
global_decision <- NULL
if(is.null(alpha)){
alpha_length <- 2
}
else{
alpha_length <- length(alpha)
}
for(i in 1:alpha_length){
global_decision1 <- result$global_decision[[i]][upper.tri(result$global_decision[[i]])]
global_decision <- cbind(global_decision, global_decision1)
}
if(is.null(alpha)){
colnames(global_decision) <- c("global_decision_0.05","global_decision_0.1")
}
else{
for(i in 1:alpha_length){
colnames(global_decision)[i] <- paste("global_decision",alpha[i],sep="_")
}
}
corr_table <- cbind(pair, precision, partialCor, CI_low_precision, CI_high_precision, z_score_precision, p_precision, global_decision)
colnames(corr_table) <- c("gene1","gene2","precision","partialCor","CI_low_precision","CI_high_precision","z_score_precision","p_precision",colnames(global_decision))
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_D-S_GL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
else{
cytoscape_format_table$threshold <- result$threshold
cytoscape_format_table$FDR <- result$FDR
cytoscape_format_table$power <- result$power
global_decision <- NULL
if(is.null(alpha)){
alpha_length <- 2
}
else{
alpha_length <- length(alpha)
}
for(i in 1:alpha_length){
global_decision1 <- result$global_decision[[i]][upper.tri(result$global_decision[[i]])]
global_decision <- cbind(global_decision, global_decision1)
}
if(is.null(alpha)){
colnames(global_decision) <- c("global_decision_0.05","global_decision_0.1")
}
else{
for(i in 1:alpha_length){
colnames(global_decision)[i] <- paste("global_decision",alpha[i],sep="_")
}
}
corr_table <- cbind(pair, precision, partialCor, CI_low_precision, CI_high_precision, z_score_precision, p_precision, global_decision)
colnames(corr_table) <- c("gene1","gene2","precision","partialCor","CI_low_precision","CI_high_precision","z_score_precision","p_precision",colnames(global_decision))
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_D-S_GL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
}
}
if(method == "GFC_SL"){
pair <- melt(upper.tri(result$T_stat))
pair <- pair[pair[,3] %in% TRUE,c(1,2)]
row.names(pair) <- NULL
T_stat <- result$T_stat[upper.tri(result$T_stat)]
if(is.null(true_graph)){
cytoscape_format_table$threshold <- result$threshold
cytoscape_format_table$FDR <- result$FDR
global_decision <- NULL
if(is.null(alpha)){
alpha_length <- 2
}
else{
alpha_length <- length(alpha)
}
for(i in 1:alpha_length){
global_decision1 <- result$global_decision[[i]][upper.tri(result$global_decision[[i]])]
global_decision <- cbind(global_decision, global_decision1)
}
if(is.null(alpha)){
colnames(global_decision) <- c("global_decision_0.05","global_decision_0.1")
}
else{
for(i in 1:alpha_length){
colnames(global_decision)[i] <- paste("global_decision",alpha[i],sep="_")
}
}
corr_table <- cbind(pair, T_stat, global_decision)
colnames(corr_table) <- c("gene1","gene2","test_statistic",colnames(global_decision))
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_GFC_SL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
else{
cytoscape_format_table$threshold <- result$threshold
cytoscape_format_table$FDR <- result$FDR
cytoscape_format_table$power <- result$power
global_decision <- NULL
if(is.null(alpha)){
alpha_length <- 2
}
else{
alpha_length <- length(alpha)
}
for(i in 1:alpha_length){
global_decision1 <- result$global_decision[[i]][upper.tri(result$global_decision[[i]])]
global_decision <- cbind(global_decision, global_decision1)
}
if(is.null(alpha)){
colnames(global_decision) <- c("global_decision_0.05","global_decision_0.1")
}
else{
for(i in 1:alpha_length){
colnames(global_decision)[i] <- paste("global_decision",alpha[i],sep="_")
}
}
corr_table <- cbind(pair, T_stat, global_decision)
colnames(corr_table) <- c("gene1","gene2","test_statistic",colnames(global_decision))
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_GFC_SL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
}
if(method == "GFC_L"){
pair <- melt(upper.tri(result$T_stat))
pair <- pair[pair[,3] %in% TRUE,c(1,2)]
row.names(pair) <- NULL
T_stat <- result$T_stat[upper.tri(result$T_stat)]
if(is.null(true_graph)){
cytoscape_format_table$threshold <- result$threshold
cytoscape_format_table$FDR <- result$FDR
global_decision <- NULL
if(is.null(alpha)){
alpha_length <- 2
}
else{
alpha_length <- length(alpha)
}
for(i in 1:alpha_length){
global_decision1 <- result$global_decision[[i]][upper.tri(result$global_decision[[i]])]
global_decision <- cbind(global_decision, global_decision1)
}
if(is.null(alpha)){
colnames(global_decision) <- c("global_decision_0.05","global_decision_0.1")
}
else{
for(i in 1:alpha_length){
colnames(global_decision)[i] <- paste("global_decision",alpha[i],sep="_")
}
}
corr_table <- cbind(pair, T_stat, global_decision)
colnames(corr_table) <- c("gene1","gene2","test_statistic",colnames(global_decision))
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_GFC_L.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
else{
cytoscape_format_table$threshold <- result$threshold
cytoscape_format_table$FDR <- result$FDR
cytoscape_format_table$power <- result$power
global_decision <- NULL
if(is.null(alpha)){
alpha_length <- 2
}
else{
alpha_length <- length(alpha)
}
for(i in 1:alpha_length){
global_decision1 <- result$global_decision[[i]][upper.tri(result$global_decision[[i]])]
global_decision <- cbind(global_decision, global_decision1)
}
if(is.null(alpha)){
colnames(global_decision) <- c("global_decision_0.05","global_decision_0.1")
}
else{
for(i in 1:alpha_length){
colnames(global_decision)[i] <- paste("global_decision",alpha[i],sep="_")
}
}
corr_table <- cbind(pair, T_stat, global_decision)
colnames(corr_table) <- c("gene1","gene2","test_statistic",colnames(global_decision))
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_GFC_L.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
}
if(method == "B_NW_SL"){
pair <- melt(upper.tri(result$precision))
pair <- pair[pair[,3] %in% TRUE,c(1,2)]
row.names(pair) <- NULL
precision <- result$precision[upper.tri(result$precision)]
partialCor <- result$partialCor[upper.tri(result$partialCor)]
CI_low_precision <- result$CI_low_precision[upper.tri(result$CI_low_precision)]
CI_high_precision <- result$CI_high_precision[upper.tri(result$CI_high_precision)]
CI_low_partialCor <- result$CI_low_partialCor[upper.tri(result$CI_low_partialCor)]
CI_high_partialCor <- result$CI_high_partialCor[upper.tri(result$CI_high_partialCor)]
z_score_precision <- result$z_score_precision[upper.tri(result$z_score_precision)]
z_score_partialCor <- result$z_score_partialCor[upper.tri(result$z_score_partialCor)]
p_precision <- result$p_precision[upper.tri(result$p_precision)]
p_partialCor <- result$p_partialCor[upper.tri(result$p_partialCor)]
if(global == FALSE){
corr_table <- cbind(pair, precision, partialCor, CI_low_precision, CI_high_precision, CI_low_partialCor, CI_high_partialCor, z_score_precision, z_score_partialCor, p_precision, p_partialCor)
colnames(corr_table) <- c("gene1","gene2","precision","partialCor","CI_low_precision","CI_high_precision", "CI_low_partialCor", "CI_high_partialCor", "z_score_precision", "z_score_partialCor", "p_precision", "p_partialCor")
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_B_NW_SL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
else{
if(is.null(true_graph)){
cytoscape_format_table$threshold <- result$threshold
cytoscape_format_table$FDR <- result$FDR
global_decision <- NULL
if(is.null(alpha)){
alpha_length <- 2
}
else{
alpha_length <- length(alpha)
}
for(i in 1:alpha_length){
global_decision1 <- result$global_decision[[i]][upper.tri(result$global_decision[[i]])]
global_decision <- cbind(global_decision, global_decision1)
}
if(is.null(alpha)){
colnames(global_decision) <- c("global_decision_0.05","global_decision_0.1")
}
else{
for(i in 1:alpha_length){
colnames(global_decision)[i] <- paste("global_decision",alpha[i],sep="_")
}
}
corr_table <- cbind(pair, precision, partialCor, CI_low_precision, CI_high_precision, CI_low_partialCor, CI_high_partialCor, z_score_precision, z_score_partialCor, p_precision, p_partialCor, global_decision)
colnames(corr_table) <- c("gene1","gene2","precision","partialCor","CI_low_precision","CI_high_precision", "CI_low_partialCor", "CI_high_partialCor", "z_score_precision", "z_score_partialCor", "p_precision", "p_partialCor", colnames(global_decision))
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_B_NW_SL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
else{
cytoscape_format_table$threshold <- result$threshold
cytoscape_format_table$FDR <- result$FDR
cytoscape_format_table$power <- result$power
global_decision <- NULL
if(is.null(alpha)){
alpha_length <- 2
}
else{
alpha_length <- length(alpha)
}
for(i in 1:alpha_length){
global_decision1 <- result$global_decision[[i]][upper.tri(result$global_decision[[i]])]
global_decision <- cbind(global_decision, global_decision1)
}
if(is.null(alpha)){
colnames(global_decision) <- c("global_decision_0.05","global_decision_0.1")
}
else{
for(i in 1:alpha_length){
colnames(global_decision)[i] <- paste("global_decision",alpha[i],sep="_")
}
}
corr_table <- cbind(pair, precision, partialCor, CI_low_precision, CI_high_precision, CI_low_partialCor, CI_high_partialCor, z_score_precision, z_score_partialCor, p_precision, p_partialCor, global_decision)
colnames(corr_table) <- c("gene1","gene2","precision","partialCor","CI_low_precision","CI_high_precision", "CI_low_partialCor", "CI_high_partialCor", "z_score_precision", "z_score_partialCor", "p_precision", "p_partialCor", colnames(global_decision))
if(!is.null(colnames(x))){
gene_symbol <- colnames(x)
corr_table[,1] <- gene_symbol[as.numeric(corr_table[,1])]
corr_table[,2] <- gene_symbol[as.numeric(corr_table[,2])]
}
cytoscape_format_table$cytoscape_format_table <- corr_table
if(csv_save == TRUE){
cat("Save the Cytoscape format table. \n")
if(is.null(directory)){
directory <- tempdir()
cat("The directory is not specified, so we use a temporary directory from the R session. \n")
cat("The directory is ", directory, ".\n",sep = "")
}
else{
cat("The directory is specified and it is ", directory, ".\n",sep = "")
}
write.csv(corr_table,file=paste(directory, "Cytoscape_B_NW_SL.csv", sep = "/"),row.names = FALSE)
}
return(cytoscape_format_table)
}
}
}
}
}
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