Gene co-expression network construction

Question

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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?

Answer 1

[WouterDeCoster]

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.