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

In LihuaJulieZhu/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

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,
  removeAncestorByPval = NULL,
  keepByLevel = NULL
)

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.
removeAncestorByPval	Remove ancestor by p-value. P-value is calculated by fisher exact test. If gene number in all of the children is significant greater than it in parent term, the parent term will be removed from the list.
keepByLevel	If the shortest path from the go term to 'all' is greater than the given level, the term will be removed.

Value

A list with 3 elements

list("bp")	enriched 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
list("mf")	enriched 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
list("cc")	enriched 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

Author(s)

Lihua Julie Zhu

References

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

See Also

phyper, hyperGtest

Examples

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

LihuaJulieZhu/ChIPpeakAnno documentation built on Aug. 5, 2020, 12:02 a.m.