我有以下问题
WGCNA - http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/
处理第 1.6 节，将网络导出到外部软件 (Cytoscape)
我目前正在尝试对一组基因执行 WGCNA，但我无法获得每个模块的 top x hub 基因。我正在尝试将网络导出到 Cytoscape，并使用与导出到 VisANT 概述的相同方法来获取 top x hub 基因。
# Select modules (only interested in one for now)
modules = c("greenyellow")
# Select module probes
probes = names(datExpr)
inModule = is.finite(match(bwModuleColors, modules))
modProbes = probes[inModule]
modGenes = annot$gene_symbols[match(modProbes, annot$geneID)]
# Select the corresponding Topological Overlap
modTOM = TOM[inModule, inModule]
dimnames(modTOM) = list(modProbes, modProbes)
# Restrict the network to the top 30 genes
nTop = 30
IMConn = softConnectivity(datExpr[, modProbes]
top = (order(-IMConn) <= nTop)
# Export the network into a fomat that Cytoscape can read
cyt = exportNetworkToCytoscape(modTOM[top, top],
edgeFile = paste("CytoscapeInput-edges-", paste(modules, collapse="-"), ".txt", sep = ""),
nodeFile = paste("CytoscapeInput-nodes-", paste(modules, collapse="-"), ".txt", sep = ""),
weight = TRUE,
threshold = 0.02,
nodeNames = modProbes,
altNodeNames = modGenes,
nodeAttr = bwModuleColors[inModule])
我写了一个短循环来计算每个基因的连接数，它按预期工作，但第 x 个基因始终有零连接。假设 x 为 30。如果我将截止值增加到 31 个中心基因，则第 30 个基因现在显示与网络中其他基因的连接，但第 31 个基因没有显示任何内容。此外，这种变化增加并减少了与网络中其他基因的一些连接数。这真的让我很困扰，因为应该只添加连接，因为网络变大了一个基因，而变化应该由第 30 个基因来解释，但输出的情况并非如此。
# Split the cytoscape file into two parts: edge and node
node <- cyt$nodeData
edge <- cyt$edgeData
# The limit covers all of the connections in the edge file by determining the length of the column ‘fromNode’
limit <- length(edge$fromNode)
# Create an empty list to store the counts for each gene
counts = list()
# Loop for the genes going from 1 to the number of genes specified for the network, ‘nTop’
for (i in 1:nTop) {
# Reset the count for each new gene and specify the names of the gene of interest and the matching genes
name = node$nodeName[[i]]
count = 0
# Nested loop that searches for matches to the gene in question in both the ‘fromNode’ and ‘toNode’columns, and adds one to the count for each match.
for (j in 1:limit) {
matchName1 = edge$fromNode[[j]]
matchName2 = edge$toNode[[j]]
if (name == matchName1 || name == matchName2)
{count = count + 1}
}
# Create a string for the attribute in the correct format
attribute <- paste(name, "=", count)
# Adds the count to the list
counts <- c(counts, attribute)
}
# End of loop
循环似乎按预期工作，所以我认为问题出在网络建设上。我目前正在回顾我对线性代数、矩阵和拓扑的了解，以尝试查看问题是否在于它们的排序方式或类似的方式，但这可能只是 exportNetworkToCytoscape() 函数的方式作品。