View source: R/3_feature_network.R
generate_feature_network | R Documentation |
generate_feature_network()
generates a network of target genes that are regulated
by the previously generated TFs, and also a separate network of housekeeping genes (HKs).
feature_network_default()
is used to configure parameters pertaining this process.
generate_feature_network(model) feature_network_default( realnet = NULL, damping = 0.01, target_resampling = Inf, max_in_degree = 5 )
model |
A dyngen intermediary model for which the transcription network has been generated with |
realnet |
The name of a gene regulatory network (GRN) in realnets.
If |
damping |
A damping factor used for the page rank algorithm used to subsample the realnet. |
target_resampling |
How many targets / HKs to sample from the realnet per iteration. |
max_in_degree |
The maximum in-degree of a target / HK. |
A dyngen model.
dyngen on how to run a complete dyngen simulation
model <- initialise_model( backbone = backbone_bifurcating(), feature_network = feature_network_default(damping = 0.1) ) data("example_model") model <- example_model %>% generate_tf_network() %>% generate_feature_network() plot_feature_network(model)
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