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

In birta: Bayesian Inference of Regulation of Transcriptional Activity

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.

Author(s)

Benedikt Zacher ([e-mail])

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)

birta documentation built on April 28, 2020, 7:27 p.m.