madzafv
commented
2 years ago What I worked out was this
netLast = getDownstreamNetwork(
tissue = "AreaXLast",
n.iterations = 50,
min.exchanged.genes = 20,
t(normalized_counts),
beta = -1,
job.path = "/u/project/gxxiao3/madzayas/BFRNASeq/BFaligned",
min.cluster.size = 30,
net.type = "signed",
debug = F,
blockTOM = F,
save.tom = T,
save.plots = T,
excludeGrey = TRUE,
fullAnnotation = T,
silent = T
)
net <- readRDS("/u/project/gxxiao3/madzayas/BFRNASeq/BFaligned/netAreaXLast.5.it.50.rds")
TOM <- readRDS("/u/project/gxxiao3/madzayas/BFRNASeq/BFaligned/netAreaXLast.5.it.50.rds.tom.rds")
# Select modules
modules = c("cyan")
# Select module genes
probes = names(net$adjacency)
inModule = is.finite(match(net$moduleColors, modules));
modGenes = probes[inModule];
# Select the corresponding Topological Overlap
dimnames(TOM2) = list(names(net$adjacency),names(net$adjacency))
modTOM = TOM2[inModule, inModule];
# Export the network into edge and node list files Cytoscape can read
cyt = exportNetworkToCytoscape(modTOM,
edgeFile = paste("CytoscapeInput-edges-", ".tsv", sep=""),
nodeFile = paste("CytoscapeInput-nodes-", ".tsv", sep=""),
weighted = TRUE,
threshold = 0.1,
nodeNames = modGenes,
nodeAttr = net$moduleColors[inModule]);
edges <- read.table(file = 'CytoscapeInput-edges-.tsv', sep = '\t', header = TRUE)
nodes <- read.table(file = 'CytoscapeInput-nodes-.tsv', sep = '\t', header = TRUE)
write.csv(x=edges, file="CytoscapeInput-edges.csv")
write.csv(x=nodes, file="CytoscapeInput-nodes.csv")
Hi, I have generated my network, which I believe it is contained in the rds obj, but I'm having a hard time finding a way of converting into something that can be read by gephi. Does CoExpNets has a function to do that? Thank you!