BICORN {BICORN}

BICORN Algorithm Function

Description

Function 'BICORN' infers a posterior module-gene regulatory network by iteratively sampling regulatory strength, transcription factor activity and several key model parameters.

Usage

BICORN(BICORN_input = NULL, L = 100, output_threshold = 10)

Arguments

BICORN_input

this list structure contains TF symbols, gene symbols and candidate modules

L

total rounds of Gibbs Sampling.

output_threshold

number of rounds after which we start to record results.

Examples

# load in the sample data input
data("sample.input")

# Data initialization (Integerate prior binding network and gene expression data)
BICORN_input<-data_integration(Binding_matrix = Binding_matrix, Binding_TFs = Binding_TFs,
Binding_genes = Binding_genes, Exp_data = Exp_data, Exp_genes = Exp_genes,
Minimum_gene_per_module_regulate = 2)

# Infer cis-regulatory modules (TF combinations) and their target genes
BICORN_output<-BICORN(BICORN_input, L = 2, output_threshold = 1)