Constructs an undirected feature–feature or feature–exposure correlation network
from correlation results stored in a MultiAssayExperiment
object. The function
supports multiple correlation formats depending on feature_type
, and stores or returns
an igraph
object with associated node and edge metadata.
Arguments
- expomicset
A
MultiAssayExperiment
object containing correlation results in metadata.- feature_type
Type of correlation result to convert to a network. One of:
"degs"
,"omics"
,"factors"
,"factor_features"
,"exposures"
,"degs_feature_cor"
,"omics_feature_cor"
, or"factor_features_feature_cor"
.- action
Whether to
"add"
the network to the object or"get"
it as a list.
Value
If action = "add"
, returns the updated MultiAssayExperiment
with a new network
entry in metadata.
If action = "get"
, returns a list with graph
(an igraph
object) and summary
(a tibble).
Details
The function detects the appropriate edge and node structure based on column names in the correlation results. Edge weights are based on correlation coefficients and include FDR values.
Examples
if (FALSE) { # \dontrun{
expomicset <- run_correlation(expomicset, feature_type = "omics", feature_cors = TRUE)
expomicset <- run_create_network(expomicset, feature_type = "omics_feature_cor")
net <- run_create_network(expomicset, feature_type = "omics_feature_cor", action = "get")
plot(net$graph)
} # }