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

Description Usage Arguments Details Value Examples

View source: R/priming_graph.R

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

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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

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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 Nov. 27, 2020, 1:27 a.m.