priming_graph: Converts the given dataframe using first variable as...

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

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.

Description

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.

Usage

priming_graph(
  df,
  competing_count,
  miRNA_count,
  aff_factor = dummy,
  deg_factor = dummy
)

Arguments

df	A data frame that includes the miRNA and competing targets.
competing_count	The counts (or expression) of competing elements of the dataset.
miRNA_count	The counts (or expression) of repressive element (miRNA) of the dataset.
aff_factor	The parameter/s of binding between miRNA and targets.
deg_factor	The parameter/s for degradation of bound miRNA:target complex.

Details

priming_graph provides grouping of competing targets and evaluation of targets within the groups taking into account miRNA:target, target:total target, interaction and degradation parameters. The target groups are determined according to miRNAs. If the factors that are important in target interactions are specified as arguments, the factors also are evaluated separately within each group. priming_graph also calculates the miRNA efficiency in steady-state conditions. It is assumed that quantity of competing targets and miRNAs are shown in the steady-state system after the miRNAs exhibit repressive efficiency. Note that the data must not include missing values such as NA or '-'.

Value

the graph object.

Examples

data('minsamp')

priming_graph(minsamp, Competing_expression, miRNA_expression)

priming_graph(minsamp, Competing_expression, miRNA_expression,
    aff_factor = c(seed_type,energy), deg_factor = region)

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