Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

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Documentation for package ‘ceRNAnetsim’ version 1.10.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

calc_perturbation	Calculates average expression changes of all nodes except trigger and finds the perturbed node count for a given node.
find_affected_nodes	Finds top affected nodes for perturbation from a particular node
find_iteration	Finds the iteration which provides maximum affected node number
find_node_perturbation	Calculates average expression changes of all (or specified) nodes except trigger and finds the perturbed node count for all (or specified) nodes in system.
find_targeting_nodes	Finds potential affecting node for given particular target.
huge_example	huge example
midsamp	midsamp
midsamp_new_counts	midsamp_new_counts
minsamp	minsamp
mirtarbasegene	mirtarbasegene
new_counts	new_counts
priming_graph	Converts the given dataframe using first variable as competing and the second as miRNA. The function converts the given dataframe using first variable as competing and the second as miRNA. If user defines interaction factors as affinity or degradation, the factors are taken into account.
simulate	Utilizes the change in expression value/s as triggering.
simulate_vis	Provides visualisation of the graph in addition to simulate function.
TCGA_E9_A1N5_mirnanormal	TCGA_E9_A1N5_mirnanormal
TCGA_E9_A1N5_mirnatumor	TCGA_E9_A1N5_mirnatumor
TCGA_E9_A1N5_normal	TCGA_E9_A1N5_normal
TCGA_E9_A1N5_tumor	TCGA_E9_A1N5_tumor
update_how	Converts the count value of the given node.
update_nodes	Carries variables from edge to node.
update_variables	Replaces new values with previous values of competing or miRNA counts.
vis_graph	Provides visualisation of the graph.