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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,41 @@ | ||
| #' @title Compute and rank TFs in network | ||
| #' | ||
| #' @param weightDT The weight data table of network | ||
| #' @param directedGraph If GRN is directed or not | ||
| #' @param weight_table The weight data table of network | ||
| #' @param directed If GRN is directed or not | ||
| #' | ||
| #' @return A data.table with three columns | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| #' library(inferCSN) | ||
| #' data("exampleMatrix") | ||
| #' weightDT <- inferCSN(exampleMatrix) | ||
| #' ranks <- compute.gene.rank(weightDT) | ||
| #' data("example_matrix") | ||
| #' weight_table <- inferCSN(example_matrix) | ||
| #' ranks <- compute.gene.rank(weight_table) | ||
| #' head(ranks) | ||
| #' | ||
| compute.gene.rank <- function(weightDT, | ||
| directedGraph = FALSE) { | ||
| colnames(weightDT) <- c("regulatory", "target", "weight") | ||
| weightDT$weight <- abs(weightDT$weight) | ||
| tfnet <- igraph::graph_from_data_frame(weightDT, directed = directedGraph) | ||
| pageRank <- data.frame(igraph::page_rank(tfnet, directed = directedGraph)$vector) | ||
| colnames(pageRank) <- c("pageRank") | ||
| pageRank$gene <- rownames(pageRank) | ||
| pageRank <- pageRank[, c("gene", "pageRank")] | ||
| pageRank <- pageRank[order(pageRank$pageRank, decreasing = TRUE), ] | ||
| pageRank$isRegulator <- FALSE | ||
| pageRank$isRegulator[pageRank$gene %in% unique(weightDT$regulatory)] <- TRUE | ||
| return(pageRank) | ||
| compute.gene.rank <- function( | ||
| weight_table, | ||
| directed = FALSE) { | ||
| colnames(weight_table) <- c("regulatory", "target", "weight") | ||
| weight_table$weight <- abs(weight_table$weight) | ||
| tfnet <- igraph::graph_from_data_frame( | ||
| weight_table, | ||
| directed = directed | ||
| ) | ||
| page_rank_res <- data.frame( | ||
| igraph::page_rank(tfnet, directed = directed)$vector | ||
| ) | ||
| colnames(page_rank_res) <- c("pageRank") | ||
| page_rank_res$gene <- rownames(page_rank_res) | ||
| page_rank_res <- page_rank_res[, c("gene", "pageRank")] | ||
| page_rank_res <- page_rank_res[order( | ||
| page_rank_res$pageRank, | ||
| decreasing = TRUE | ||
| ), ] | ||
| page_rank_res$isRegulator <- FALSE | ||
| page_rank_res$isRegulator[ | ||
| page_rank_res$gene %in% unique( | ||
| weight_table$regulatory | ||
| ) | ||
| ] <- TRUE | ||
| return(page_rank_res) | ||
| } |
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