enrichment_analysis {BioNERO} | R Documentation |
Perform enrichment analysis for a set of genes
enrichment_analysis( genes, background_genes, annotation, column = NULL, correction = "BH", p = 0.05, bp_param = BiocParallel::SerialParam() )
genes |
Character vector containing genes for overrepresentation analysis. |
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() |
Data frame containing significant terms, p-values and associated genes.
Fabricio Almeida-Silva
data(filt.se) data(zma.interpro) genes <- rownames(filt.se)[1:50] background_genes <- rownames(filt.se) annotation <- zma.interpro # Using p = 1 to show all results enrich <- enrichment_analysis(genes, background_genes, annotation, p = 1)