Entering edit mode
4.9 years ago
hennet.lauriane
▴
40
Hi,
I want to calculate centrality score using my network from WGCNA.
I have a edge file consisting of two columns of gene names. Every line represents a connection.
FromNode toNode
gene1 gene2
gene3 gene2
gene4 gene1
gene4 gene3
etc
I transformed this edge file into a igraph g object with
> el=as.matrix(edgelistpink)
> el[,1]=as.character(el[,1])
> el[,2]=as.character(el[,2])
> g=graph.edgelist(el,directed=FALSE)
I then calculated the degree using
calculate_centralities(g, include="Degree Centrality")
The ouput is
[1] 17 134 111 130 149 119 164 152 175 156 63 171 190 146 103 167 125 173 8 167 20 60
[23] 49 142 79 75 68 54 11 11 51 95 14 67 2 19 14 23 16 18 24 82 18 23
[45] 8 6 65 34 20 33 17 11 12 24 25 5 79 37 37 77 25 35 26 6 12 21
[67] 13 21 14 47 29 33 11 27 20 12 11 23 28 3 33 13 12 19 14 17 14 21etc
I assume it is a list of every Degree Centrality for every node in my network (gene 1 to gene 4)
How can I know in which order are my node/genes, how to recover the vector list of genes that was used for the degree centrality calculation. All this in order to know wich centrality score to allocate to with gene ?
Thank you !