data_integration: Data Initialization for BICORN

In BICORN: Integrative Inference of De Novo Cis-Regulatory Modules

Description

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.

Usage

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)

BICORN documentation built on May 2, 2019, 2:05 a.m.