\name{addGeneIDs}
\Rdversion{1.1}
\alias{addGeneIDs}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{
Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq id.
}
\description{
Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq id leveraging organism annotation dataset! For example, org.Hs.eg.db is the dataset from orgs.Hs.eg.db package for human, while org.Mm.eg.db is the dataset from the org.Mm.eg.db package for mouse}
\usage{
addGeneIDs(annotatedPeak, orgAnn, IDs2Add=c("symbol"), feature_id_type="ensembl_gene_id",silence=TRUE)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{annotatedPeak}{RangedData such as data(annotatedPeak) or a vector of feature IDs}
  \item{orgAnn}{organism annotation dataset such as org.Hs.eg.db}
  \item{IDs2Add}{a vector of annotation identifiers to be added such as accnum, ensembl, ensemblprot, ensembltrans, entrez_id, enzyme, genename, pfam, pmid, prosite, refseq, symbol, unigene, and uniprot.}
  \item{feature_id_type}{type of ID: can be ensemble_gene_id, entrez_id, gene_symbol, gene_alias or refseq_id}
  \item{silence}{TRUE or FALSE. If TRUE, will not show unmapped entrez id for feature ids.}
}
\details{
	Parameter IDs2Add can be set to any combination of identifiers such as "accnum","ensembl","ensemblprot","ensembltrans","entrez_id","enzyme","genename","pfam","pmid","prosite","refseq","symbol","unigene" and "uniprot". Some IDs are unique to a organism, such as "omim" for org.Hs.eg.db and "mgi" for org.Mm.eg.db.

	Here is the definition of different IDs : 

	accnum: GenBank accession numbers

	ensembl: Ensembl gene accession numbers

	ensemblprot: Ensembl protein accession numbers

	ensembltrans: Ensembl transcript accession numbers

	entrez_id: entrez gene identifiers

	enzyme: EC numbers

	genename: gene name

	pfam: Pfam identifiers

	pmid: PubMed identifiers

	prosite: PROSITE identifiers

	refseq: RefSeq identifiers

	symbol: gene abbreviations

	unigene: UniGene cluster identifiers

	uniprot: Uniprot accession numbers

	omim: OMIM(Mendelian Inheritance in Man) identifiers

	mgi: Jackson Laboratory MGI gene accession numbers
}
\value{
RangedData if the input is a RangedData or dataframe with added IDs if input is a character vector.
}
\references{
http://www.bioconductor.org/packages/release/data/annotation/
}
\author{
Jianhong Ou, Lihua Julie Zhu
}
\note{
}

\seealso{

}
\examples{
data(annotatedPeak)
library(org.Hs.eg.db)
addGeneIDs(annotatedPeak[1:6,],"org.Hs.eg.db",c("symbol","omim"))
addGeneIDs(annotatedPeak$feature[1:6],"org.Hs.eg.db",c("symbol","genename"))
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{ misc }