enrich_go: Enriched ontologies for recognized organisms

In OceaneCsn/DIANE: DIANE

Enriched ontologies for recognized organisms

Description

This function returns the enriched biological processes in a set of genes, as compared to a background set of genes. The GO terms are retreived by the clusterProfiler package and the bioconductor organism databases (for example org.At.tair.db). The frequencies comparisons between GO terms in the genes of interest and the background are performed using Fischer tests, with 0.05 adjusted pvalues threshold. Those significantly enriched GO terms are then simplified with a semantic similarity threshold that can be chosen. It returns a dataframe containing, for each significant GO, their gene count, gene symbols, adjusted pvalue, description, etc.

Usage

enrich_go(
  genes,
  background,
  org = org.At.tair.db::org.At.tair.db,
  sim_cutoff = 0.85,
  GO_type = "BP",
  fdr = 0.05,
  pval = 0.05
)

Arguments

genes	gene set of interest. MUST be entrez IDs, that can be obtained from DIANE's functions convert_from_X(gene_IDs) depending on your organism. If your gene IDs are splicing aware, remove this information before with get_locus(gene_IDs).
background	gene set considered as the "universe" against which perfom the tests. MUST be entrez IDS that can be obtained from DIANE's functions convert_from_X(gene_IDs) depending on your organism. If your gene IDs are splicing aware, remove this information before with get_locus(gene_IDs).
org	organism, in the format of bioconductor organisms databases (e.g org.xx.xx.db). Possible values are, for DIANE's recognized organisms : org.Mm.eg.db, org.Hs.eg.db, org.Dm.eg.db, org.Ce.eg.db, org.EcK12.eg.db, org.At.tair.db
sim_cutoff	similarity cutoff to use for pooling similar GO terms
GO_type	character between BP (Biological Process), CC(Cellular Component) or MF (Molecular Function), depending on the GO subtype to use in the analysis
fdr	adjusted pvalues threshold, default id 0.05
pval	pvalues threshold, default id 0.05

Value

data.frame with gene significant gene ontologies, and their characteristics as columns

Examples

data("abiotic_stresses")
genes <- abiotic_stresses$heat_DEGs

genes <- get_locus(genes)
background <- get_locus(rownames(abiotic_stresses$normalized_counts))

genes <- convert_from_agi(genes)
background <- convert_from_agi(background)

go <- enrich_go(genes, background)
head(go)

OceaneCsn/DIANE documentation built on Jan. 10, 2024, 6:43 p.m.