View source: R/reconstruct_network.R
network_analysis | R Documentation |
This function calculates the significant transcription factors and significant regulatory relationships in each module through hypergeometric tests to construct regulatory networks
network_analysis(
regulatory_relationships,
Kmeans_result,
TFFDR1 = 2,
TFFDR2 = 2,
ModuleFDR = 0.05
)
regulatory_relationships |
Refined or unrefined regulatory relationships.
Unrefined regulatory relationships are generated by |
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 |
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
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)
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