Question: CINNA centrality score and retrieving node names
0
gravatar for hennet.lauriane
17 months ago by
hennet.lauriane40 wrote:

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 !

ADD COMMENTlink written 17 months ago by hennet.lauriane40
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