Description Usage Arguments Details Value Author(s) References See Also Examples
Internal function, creates a two-column network matrix that can be further processed by neat
.
1 | networkmatrix(network, nodes, nettype)
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network |
One of the following objects: an adjacency matrix (class |
nodes |
Vector containing the (ordered) names of all nodes in the network |
nettype |
Either |
This is an internal function, that is called within neat
to convert different types of network objects (see argument 'network' above) into a standard two-column network matrix, that can then be processed by neat
.
A two-column matrix, where every row represents and edge. For directed networks, parent nodes must be in the first column, and child nodes in the second.
Mirko Signorelli
Signorelli, M., Vinciotti, V., Wit, E. C. (2016). NEAT: an efficient network enrichment analysis test. BMC Bioinformatics, 17:352. Url: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1203-6.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | # First case: adjacency matrix
n<-50
adjacency <- matrix(sample(0:1, n^2, replace=TRUE, prob=c(0.9,0.1)), ncol=n)
diag(adjacency) <- 0
lab = paste(rep('gene'),1:n)
head(networkmatrix(adjacency, lab, 'directed'))
# Second case: sparse adjacency matrix
library(Matrix)
sparse_adjacency<-Matrix(adjacency,sparse=TRUE)
head(networkmatrix(sparse_adjacency, lab, 'directed'))
# Third case: igraph object
library(igraph)
igraph_graph = erdos.renyi.game(15, 1/3)
lab = paste(rep('gene'),1:15)
head(networkmatrix(igraph_graph, lab, 'directed'))
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