getEnrichedGO

0th

Percentile

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

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

Keywords
misc
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
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

See Also

phyper, hyperGtest

Aliases
  • getEnrichedGO
Examples
  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
}
Documentation reproduced from package ChIPpeakAnno, version 3.6.5, License: GPL (>= 2)

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