enrichmentAnalysis: Gene ontology enrichment analysis

View source: R/enrichmentAnalysis.R

enrichmentAnalysisR Documentation

Gene ontology enrichment analysis

Description

GO enrichment analysis for nodes

Usage

enrichmentAnalysis(
  node_regions,
  orgDb,
  onto = c("BP", "CC", "MF"),
  minGeneNum = 3,
  evidence = list(Experimental_evidence_codes = c("EXP", "IDA", "IPI", "IMP", "IGI",
    "IEP", "HTP", "HDA", "HMP", "HGI", "HEP"), `Phylogenetically-inferred_annotations` =
    c("IBA", "IBD", "IKR", "IRD"), Computational_analysis_evidence_codes = c("ISS",
    "ISO", "ISA", "ISM", "IGC", "RCA"), Author_statement_evidence_codes = c("TAS",
    "NAS"), Curator_statement_evidence_codes = c("IC", "ND"),
    Electronic_annotation_evidence_code = c("IEA")),
  ...
)

Arguments

node_regions

GRanges object represent regions interacted with nodes. The object must be annotated by annotateNodes with comp_id and gene_id in the metadata.

orgDb

An object of OrgDb to extract gene symbols.

onto

Ontology category.

minGeneNum

An integer(1) value indicating the minimal number of gene to start the enrichment analysis. If total gene counts is smaller than the 'minGeneNum', the NULL will be returned.

evidence

The acceptable evidence code.

...

Not used.

Value

A list with element enriched and enriched_in_compound. Or NULL if total counts of gene is smaller than 'minGeneNum'.

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## for human hg19
library(org.Hs.eg.db) ## used to convert gene_id to gene_symbol 
library(GO.db)
set.seed(123)
node_regions <- createRandomNodes(TxDb.Hsapiens.UCSC.hg19.knownGene)
node_regions <- 
    annotateNodes(node_regions,
                  TxDb.Hsapiens.UCSC.hg19.knownGene,
                  org.Hs.eg.db)
enr <- enrichmentAnalysis(node_regions, org.Hs.eg.db, onto="BP")

jianhong/GenomicInteractionHub documentation built on April 14, 2022, 10:49 a.m.