getEnrichedGO: Obtain enriched gene ontology (GO) terms that near the peaks

Description

Obtain enriched gene ontology (GO) terms based on the features near the enriched peaks using GO.db package and GO gene mapping package such as org.Hs.db.eg to obtain the GO annotation and using hypergeometric test (phyper) and multtest package for adjusting p-values

Usage

getEnrichedGO(annotatedPeak, orgAnn, feature_id_type="ensembl_gene_id", 
maxP=0.01, minGOterm=10, multiAdjMethod=NULL, condense=FALSE)

Arguments

annotatedPeak

A GRanges object or a vector of feature IDs

orgAnn

Organism annotation package such as org.Hs.eg.db for human and org.Mm.eg.db for mouse, org.Dm.eg.db for fly, org.Rn.eg.db for rat, org.Sc.eg.db for yeast and org.Dr.eg.db for zebrafish

feature_id_type

The feature type in annotatedPeak such as ensembl_gene_id, refseq_id, gene_symbol or entrez_id

maxP

The maximum p-value to be considered to be significant

minGOterm

The minimum count in a genome for a GO term to be included

multiAdjMethod

The multiple testing procedures, for details, see mt.rawp2adjp in multtest package

condense

condense the results or not.

Value

bp: enriched biological process with the following 9 variablesgo.id:GO biological process idgo.term:GO biological process termgo.Definition:GO biological process descriptionOntology: Ontology branch, i.e. BP for biological processcount.InDataset: count of this GO term in this datasetcount.InGenome: count of this GO term in the genomepvalue: pvalue from the hypergeometric testtotaltermInDataset: count of all GO terms in this datasettotaltermInGenome: count of all GO terms in the genome
mf: enriched molecular function with the following 9 variablesgo.id:GO molecular function idgo.term:GO molecular function termgo.Definition:GO molecular function descriptionOntology: Ontology branch, i.e. MF for molecular functioncount.InDataset: count of this GO term in this datasetcount.InGenome: count of this GO term in the genomepvalue: pvalue from the hypergeometric testtotaltermInDataset: count of all GO terms in this datasettotaltermInGenome: count of all GO terms in the genome
cc: enriched cellular component the following 9 variablesgo.id:GO cellular component idgo.term:GO cellular component termgo.Definition:GO cellular component descriptionOntology: Ontology type, i.e. CC for cellular componentcount.InDataset: count of this GO term in this datasetcount.InGenome: count of this GO term in the genomepvalue: pvalue from the hypergeometric testtotaltermInDataset: count of all GO terms in this datasettotaltermInGenome: count of all GO terms in the genome

References

Johnson, N. L., Kotz, S., and Kemp, A. W. (1992) Univariate Discrete Distributions, Second Edition. New York: Wiley

Examples

Run this code

  data(enrichedGO)
  enrichedGO$mf[1:10,]
  enrichedGO$bp[1:10,]
  enrichedGO$cc
  if (interactive()) {
     data(annotatedPeak)
     library(org.Hs.eg.db)
     enriched.GO = getEnrichedGO(annotatedPeak[1:6,], 
                                 orgAnn="org.Hs.eg.db", 
                                 maxP=0.01,
                                 multiAdj=FALSE, 
                                 minGOterm=10, 
                                 multiAdjMethod="")
     dim(enriched.GO$mf)
     colnames(enriched.GO$mf)
     dim(enriched.GO$bp)
     enriched.GO$cc
}