Transcription factor target enrichment test — Transcription_Factor_enrichment • Omix

Transcription factor target enrichment test

Transcription_Factor_enrichment(
  communities,
  weights,
  TF_gmt = "Enrichr_Queries.gmt",
  threshold = 1.5,
  direction = "negative"
)

Arguments

communities: communities slot generated generated by communities_network
weights: Weight list generated by extract_weights
TF_gmt: GMT file with Transcription Factors and target genes. Check https://maayanlab.cloud/chea3/
threshold: Absolute threshold to filter weights
direction: string indicating direction as "positive" or "negative"

Value

TF target enrichment in each modules

See also

Other Multi-omic integration downstream analysis: OpenTarget_dataframe(), Transcription_Factor_enrichment_supervised(), circos_TF(), clustering_DE_analysis(), extract_loadings(), extract_multiomic_signature(), extract_weigths(), integrative_results_clustering(), integrative_results_sparse_supervised(), integrative_results_supervised(), integrative_results_unsupervised(), multiomics_modules(), multiomics_network_matrix(), multiomics_network(), plot_module_trajectory(), posterior_probability(), pseudotime_inference(), sign_signature()