enrichmentAnalysis: Gene ontology enrichment analysis

In jianhong/GenomicInteractionNodes: A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

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/GenomicInteractionNodes documentation built on Oct. 28, 2023, 1:11 a.m.