list_backbones {dyngen} | R Documentation |
List of all predefined backbone models
Description
A module is a group of genes which, to some extent, shows the same expression behaviour. Several modules are connected together such that one or more genes from one module will regulate the expression of another module. By creating chains of modules, a dynamic behaviour in gene regulation can be created.
Usage
list_backbones()
backbone_bifurcating()
backbone_bifurcating_converging()
backbone_bifurcating_cycle()
backbone_bifurcating_loop()
backbone_branching(
num_modifications = rbinom(1, size = 6, 0.25) + 1,
min_degree = 3,
max_degree = sample(min_degree:5, 1)
)
backbone_binary_tree(num_modifications = rbinom(1, size = 6, 0.25) + 1)
backbone_consecutive_bifurcating()
backbone_trifurcating()
backbone_converging()
backbone_cycle()
backbone_cycle_simple()
backbone_linear()
backbone_linear_simple()
backbone_disconnected(
left_backbone = list_backbones() %>% keep(., names(.) != "disconnected") %>%
sample(1) %>% first(),
right_backbone = list_backbones() %>% keep(., names(.) != "disconnected") %>%
sample(1) %>% first(),
num_common_modules = 10
)
Arguments
num_modifications |
The number of branch points in the generated backbone. |
min_degree |
The minimum degree of each node in the backbone. |
max_degree |
The maximum degree of each node in the backbone. |
left_backbone |
A backbone (other than a disconnected backbone), see |
right_backbone |
A backbone (other than a disconnected backbone), see |
num_common_modules |
The number of modules which are regulated by either backbone. |
Value
A list of all the available backbone generators.
See Also
dyngen on how to run a dyngen simulation
Examples
names(list_backbones())
bb <- backbone_bifurcating()
bb <- backbone_bifurcating_converging()
bb <- backbone_bifurcating_cycle()
bb <- backbone_bifurcating_loop()
bb <- backbone_binary_tree()
bb <- backbone_branching()
bb <- backbone_consecutive_bifurcating()
bb <- backbone_converging()
bb <- backbone_cycle()
bb <- backbone_cycle_simple()
bb <- backbone_disconnected()
bb <- backbone_linear()
bb <- backbone_linear_simple()
bb <- backbone_trifurcating()
model <- initialise_model(
backbone = bb
)
[Package dyngen version 1.0.5 Index]