cytoscape 输入数据

  1. my_modules <- c("red")
  2. i = paste(my_modules, collapse = "_")
  4. # paste(c("red", "black", "green"), collapse = "_")
  5. # #> [1] "red_black_green"
  7. m_wgcna_result <- wgcna_result %>% filter(module %in% my_modules)
  9. m_datExpr <- datExpr[, m_wgcna_result$gene_id]
  11. # 计算该模块的 TOM 矩阵  
  12. m_TOM <- TOMsimilarityFromExpr(
  13.   m_datExpr,
  14.   power = sft$powerEstimate,
  15.   networkType = "unsigned",
  16.   TOMType = "unsigned")
  18. dimnames(m_TOM) <- list(colnames(m_datExpr), colnames(m_datExpr))
  20. edge <- paste("CytoscapeInput-network.", i, ".txt", sep = "")
  21. node <- paste("CytoscapeInput-node.", i, ".txt", sep = "")
  23. # 导出 Cytoscape 输入文件
  24. cyt <- exportNetworkToCytoscape(
  25.     m_TOM,
  26.     edgeFile = edge,
  27.     nodeFile = node,
  28.     weighted = TRUE,
  29.     threshold = 0.1)