get_networks | R Documentation |

Extracts the estimated association network for each group from the differential network analysis results.

get_networks(x)

`x` |
A 'dnapath' object from |

A list of two association matrices.

The two matrices can be plotted using the
`plot_network`

function from the SeqNet package, as
illustrated in the examples below.

data(meso) data(p53_pathways) set.seed(0) results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, group_labels = meso$groups, n_perm = 10) # Extract the two estimated association networks for the first pathway nw <- get_networks(results[[1]]) # Plot the networks using the SeqNet::plot_network function. # Note that the `compare_graph` argument is used so that the same node layout # is used across all of the plots. # Plot the two networks (in separate plots) g <- SeqNet::plot_network(nw[[1]]) SeqNet::plot_network(nw[[1]], compare_graph = g) # Plot of the differential network for pathway 1. # Again, the `compare_graph` argument is used to maintain the same layout. plot(results[[1]], compare_graph = g) # We see that genes 51230 and 7311 show strong differential connectivity. # The plot_pair() function can be used to investigate these two genes further. plot_pair(results[[1]], "51230", "7311")

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