birta (version 1.16.0)

get_potential_swaps: Calculate swap partner for TF-/miRNA-target graph.

Description

Calculates for TF-/miRNA-target graph all potential swap partner.

Usage

get_potential_swaps(genesetsTF=NULL, genesetsmiRNA=NULL, perc.overlap.cutoff = 0.8, integer.id=TRUE, verbose=TRUE)

Arguments

genesetsTF

Each entry corresponds to a TF and contains its target genes.

genesetsmiRNA

Each entry corresponds to a miRNA and contains its target genes.

perc.overlap.cutoff

Percentage cutoff of minimal overlap between two miRNAs or TFs to be possible swap partner.

integer.id

If TRUE, the swap partner are not outputted as characters, but as integer indices.

verbose

print process or not.

Value

The function returns a list, with the following entries:

T_potential_swaps

Contains for each TF all potential swap partner.

S_potential_swaps

Contains for each miRNA all potential swap partner.

Examples

genesetsTF = list("V$1"=c("A", "B", "C", "D", "E"), "V$2"=c("A", "B", "C", "D"), "V$3"=c("A", "B", "C"))
genesetsmiRNA =list("miR-1"=c("C", "E", "D", "G", "H"), "miR-2"=c("C", "E", "D", "G"), "miR-3"=c("C", "E"))
get_potential_swaps(genesetsTF, genesetsmiRNA, integer.id=FALSE, perc.overlap.cutoff=0.7)