get_association_matrix.network: Get association matrix

In SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks

Description

Get association matrix

Usage

## S3 method for class 'network'
get_association_matrix(x, tol = 10^-13, ...)

Arguments

x	Either a 'network', 'network_module', or 'matrix' object.
tol	A small tolerance threshold; any entry that is within tol from zero is set to zero.
...	Additional arguments.

Value

An association matrix with entry ij != 0 if node i and j are connected, and 0 otherwise. The diagonal entries are all zero.

Examples

# Create a random network with 10 nodes and add random edge weights.
nw <- random_network(10)
nw <- gen_partial_correlations(nw)
# Get adjacency matrix for the network or individual modules in the network.
get_association_matrix(nw)
module <- nw$modules[[1]]
get_association_matrix(module)

Example output

               1         2         3          4          5          6
 [1,]  0.0000000 0.0000000 0.0000000  0.0000000  0.0000000  0.0000000
 [2,]  0.0000000 0.0000000 0.0000000  0.0000000  0.0000000  0.0000000
 [3,]  0.0000000 0.0000000 0.0000000  0.3669184  0.3972928  0.2677742
 [4,]  0.0000000 0.0000000 0.3669184  0.0000000  0.0000000  0.0000000
 [5,]  0.0000000 0.0000000 0.3972928  0.0000000  0.0000000  0.0000000
 [6,]  0.0000000 0.0000000 0.2677742  0.0000000  0.0000000  0.0000000
 [7,] -0.3419121 0.0000000 0.4454483  0.0000000  0.0000000  0.4491131
 [8,]  0.0000000 0.3014140 0.0000000  0.0000000 -0.5090547 -0.3527970
 [9,]  0.2879340 0.3940522 0.0000000 -0.2794462  0.0000000  0.0000000
[10,]  0.4582986 0.0000000 0.0000000  0.0000000  0.0000000  0.0000000
               7          8          9        10
 [1,] -0.3419121  0.0000000  0.2879340 0.4582986
 [2,]  0.0000000  0.3014140  0.3940522 0.0000000
 [3,]  0.4454483  0.0000000  0.0000000 0.0000000
 [4,]  0.0000000  0.0000000 -0.2794462 0.0000000
 [5,]  0.0000000 -0.5090547  0.0000000 0.0000000
 [6,]  0.4491131 -0.3527970  0.0000000 0.0000000
 [7,]  0.0000000  0.3223657  0.0000000 0.3961943
 [8,]  0.3223657  0.0000000  0.0000000 0.0000000
 [9,]  0.0000000  0.0000000  0.0000000 0.0000000
[10,]  0.3961943  0.0000000  0.0000000 0.0000000
               1         2         3          4          5          6
 [1,]  0.0000000 0.0000000 0.0000000  0.0000000  0.0000000  0.0000000
 [2,]  0.0000000 0.0000000 0.0000000  0.0000000  0.0000000  0.0000000
 [3,]  0.0000000 0.0000000 0.0000000  0.3669184  0.3972928  0.2677742
 [4,]  0.0000000 0.0000000 0.3669184  0.0000000  0.0000000  0.0000000
 [5,]  0.0000000 0.0000000 0.3972928  0.0000000  0.0000000  0.0000000
 [6,]  0.0000000 0.0000000 0.2677742  0.0000000  0.0000000  0.0000000
 [7,] -0.3419121 0.0000000 0.4454483  0.0000000  0.0000000  0.4491131
 [8,]  0.0000000 0.3014140 0.0000000  0.0000000 -0.5090547 -0.3527970
 [9,]  0.2879340 0.3940522 0.0000000 -0.2794462  0.0000000  0.0000000
[10,]  0.4582986 0.0000000 0.0000000  0.0000000  0.0000000  0.0000000
               7          8          9        10
 [1,] -0.3419121  0.0000000  0.2879340 0.4582986
 [2,]  0.0000000  0.3014140  0.3940522 0.0000000
 [3,]  0.4454483  0.0000000  0.0000000 0.0000000
 [4,]  0.0000000  0.0000000 -0.2794462 0.0000000
 [5,]  0.0000000 -0.5090547  0.0000000 0.0000000
 [6,]  0.4491131 -0.3527970  0.0000000 0.0000000
 [7,]  0.0000000  0.3223657  0.0000000 0.3961943
 [8,]  0.3223657  0.0000000  0.0000000 0.0000000
 [9,]  0.0000000  0.0000000  0.0000000 0.0000000
[10,]  0.3961943  0.0000000  0.0000000 0.0000000

SeqNet documentation built on July 9, 2021, 9:08 a.m.