network_analysis: Function to make regulatory network analysis

In jiang-junyao/IReNA: IReNA

Function to make regulatory network analysis

Description

This function calculates the significant transcription factors and significant regulatory relationships in each module through hypergeometric tests to construct regulatory networks

Usage

network_analysis(
  regulatory_relationships,
  Kmeans_result,
  TFFDR1 = 2,
  TFFDR2 = 2,
  ModuleFDR = 0.05
)

Arguments

regulatory_relationships	Refined or unrefined regulatory relationships. Unrefined regulatory relationships are generated by get_cor, and you can use filter_regulation_fimo or consequence of Footprints_FOS to refine it
Kmeans_result	Kmeans result data.frame, row names should be ENSEMBEL ID, and the first column should be gene Symbol ID, the second column should be KmeansGroup
TFFDR1	numeric, indicating the cutoff (FDR) to identify enriched transcription factors
TFFDR2	numeric, indicating the cutoff (FDR) to identify enriched transcription factors that regulate each module to make regulatory network for enriched transcription factors of each module
ModuleFDR	numeric, indicating the cutoff (FDR) to identify enriched modular regulatory relationships to make intramodular regulatory network

Value

This function return a list which contain 10 element

Cor_TFs: data.frame of expressed TFs in the gene networks

Cor_EnTFs: data.frame of TFs which significantly regulate gene modules (or enriched TFs)

FOSF_RegMTF_Cor_EnTFs: regulatory pairs in which the source gene is enriched TF

FOSF_RegMTF_Cor_EnTFsTarg: regulatory pairs in which both source gene and target gene are enriched TFs

FOSF_RegMTF_Cor_EnTFsTargM: regulatory pairs only including regulations within each module but not those between modules

TF_list: enriched TFs which significantly regulate gene modules

TF_module_regulation: details of enriched TFs which significantly regulate gene modules

TF_network: regulatory network for enriched transcription factors of each module

intramodular_network: intramodular regulatory network

Examples

load(system.file("extdata", "test_clustering.rda", package = "IReNA"))
Kmeans_cluster_Ens <- add_ENSID(test_clustering,Spec1='Hs')
motif1 <- Tranfac201803_Hs_MotifTFsF
regulatory_relationships <- get_cor(Kmeans_cluster_Ens,motif1,0.7)
TFs_list <- network_analysis(regulatory_relationships,Kmeans_cluster_Ens)

jiang-junyao/IReNA documentation built on Nov. 15, 2024, 1:51 a.m.