get_networks: Get the two association networks

In dnapath: Differential Network Analysis using Gene Pathways

Get the two association networks

Description

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

Usage

get_networks(x)

Arguments

x	A 'dnapath' object from dnapath.

Value

A list of two association matrices.

Note

The two matrices can be plotted using the plot_network function from the SeqNet package, as illustrated in the examples below.

Examples

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")

dnapath documentation built on April 3, 2025, 8:32 p.m.