View source: R/enrichmentAnalysis.R
enrichmentAnalysis | R Documentation |
GO enrichment analysis for nodes
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")), ... )
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. |
A list with element enriched and enriched_in_compound. Or NULL if total counts of gene is smaller than 'minGeneNum'.
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")
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