module_enrichment {BioNERO} | R Documentation |
Perform enrichment analysis for coexpression network modules
module_enrichment( net = NULL, background_genes, annotation, column = NULL, correction = "BH", p = 0.05, bp_param = BiocParallel::SerialParam() )
net |
List object returned by |
background_genes |
Character vector of genes to be used as background for the Fisher's Exact Test. |
annotation |
Annotation data frame with genes in the first column and functional annotation in the other columns. This data frame can be exported from Biomart or similar databases. |
column |
Column or columns of |
correction |
Multiple testing correction method. One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr" or "none". Default is "BH". |
p |
P-value threshold. P-values below this threshold will be considered significant. Default is 0.05. |
bp_param |
BiocParallel back-end to be used. Default: BiocParallel::SerialParam() |
A data frame containing enriched terms, p-values, gene IDs and module names.
Fabricio Almeida-Silva
data(filt.se) data(zma.interpro) background <- rownames(filt.se) gcn <- exp2gcn(filt.se, SFTpower = 18, cor_method = "pearson") mod_enrich <- module_enrichment(gcn, background, zma.interpro, p=1)