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

A list with 3 elements
bpenriched biological process with the following 9 variables
go.id:GO biological process id go.term:GO biological process term go.Definition:GO biological process description Ontology: Ontology branch, i.e. BP for biological process
count.InDataset: count of this GO term in this dataset
count.InGenome: count of this GO term in the genome
pvalue: pvalue from the hypergeometric test
totaltermInDataset: count of all GO terms in this dataset
totaltermInGenome: count of all GO terms in the genome
mfenriched molecular function with the following 9 variables
go.id:GO molecular function id go.term:GO molecular function term go.Definition:GO molecular function description Ontology: Ontology branch, i.e. MF for molecular function
count.InDataset: count of this GO term in this dataset
count.InGenome: count of this GO term in the genome
pvalue: pvalue from the hypergeometric test
totaltermInDataset: count of all GO terms in this dataset
totaltermInGenome: count of all GO terms in the genome
ccenriched cellular component the following 9 variables
go.id:GO cellular component id go.term:GO cellular component term go.Definition:GO cellular component description Ontology: Ontology type, i.e. CC for cellular component
count.InDataset: count of this GO term in this dataset
count.InGenome: count of this GO term in the genome
pvalue: pvalue from the hypergeometric test
totaltermInDataset: count of all GO terms in this dataset
totaltermInGenome: 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
}