My file is like this -
TCGA-5557 TCGA-A6DD TCGA-A6DE TCGA-4227
HECW1 70 32 274 49
KMT2E 3344 1030 6263 2270
CACNA1G 274 23 28 3
USH1C 1 0 1 20
I want to create a gene co-expression network and using this code-
mycounts <- read.table("data.txt", header = T, sep = "\t",row.names = 1)
head(mycounts)
dim(mycounts)
library(GENIE3)
library(igraph)
library(RCy3)
library(Rgraphviz)
weight.matrix <- GENIE3(mycounts)
link.list <- linkList(weight.matrix, report.max=1000)
edge_listsi <- link.list[!duplicated(link.list),]
Gsi <- graph.data.frame(edge_listsi,directed = F)
Asi <- get.adjacency(Gsi,sparse = F,attr = "weight",type = "both")
g_arasi <- graph.adjacency(Asi,mode = "undirected",weighted = T)
g.cyto <- igraph.to.graphNEL(g_arasi)
cw = createNetworkFromGraph("net", graph=g.cyto)
displayGraph (cw)
After this-
link.list <- linkList(weight.matrix, report.max=1000)
Getting error like this-
Error in linkList(weight.matrix, report.max = 1000) :
could not find function "linkList"
How to fix this error? Or is there any other way to create a gene co-expression matrix?
I assume you are following a vignette or tutorial. Read it again, but careful. I googled, found the GENIE3 vignette, and saw that linkList() is indeed not a function. An example in that vignette is linkList <- getLinkList(weightMat, reportMax=5), which is presumably what you need.
Following this link Construct gene coexpression network , is there any other way to construct a gene co-expression network from this file? If not how to fix this error?
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