data_integration function

Data Initialization for BICORN

Function 'data_integration' integrates the prior TF-gene binding network and gene expression data together. It will remove any genes missing either TF bindings or gene expression and identify a list of candidate cis-regulatory modules.

data_integration(Binding_matrix = NULL, Binding_TFs = NULL,
  Binding_genes = NULL, Exp_data, Exp_genes = NULL,
  Minimum_gene_per_module_regulate = 2)

Arguments

• Binding_matrix: loaded prior binding network
• Binding_TFs: loaded transcription factors
• Binding_genes: loaded genes in the prior binding network
• Exp_data: loaded properly normalized gene expression data
• Exp_genes: loaded genes in the gene expression data
• Minimum_gene_per_module_regulate: the minimum number of genes regulated by each module, used for candidate module filtering.

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)