find_affected_nodes: Finds top affected nodes for perturbation from a particular...

In selcenari/ceRNAnetsim: Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

Finds top affected nodes for perturbation from a particular node

Description

Finds top affected nodes for perturbation from a particular node

Usage

find_affected_nodes(
  input_graph,
  node_name,
  how = 1,
  cycle = 1,
  limit = 0,
  top = 5
)

Arguments

input_graph	The graph object that was processed with priming_graph function.
node_name	The node to trigger perturbations.
how	The change of count (expression) of the given node in terms of fold change.
cycle	The iteration of simulation.
limit	The minimum fold change which can be taken into account for perturbation calculation on all nodes in terms of percentage.
top	Determines how many nodes most affected will be listed.

Details

Lists the most affected nodes after perturbation initiated from a particular node. In the background, it compares the calculated values after the simulation with their initial values.

Value

It gives a tibble form dataset that includes perturbation node, affected nodes and changes of them.

Examples

data('midsamp')

midsamp%>%
priming_graph(competing_count = Gene_expression, 
              miRNA_count = miRNA_expression)%>%
find_affected_nodes(node_name = "Gene1", 
                    how = 2, 
                    cycle = 2, 
                    top = 2)

selcenari/ceRNAnetsim documentation built on Feb. 14, 2024, 4:20 a.m.