converting gene ids using bioconductor with biomaRt and annotation packages

I had a post using  mygene to convert gene ids. Bioconductor can do the same job.
I put a gist on github.

	##### use bioconductor annotation packages #######
	source("http://Bioconductor.org/biocLite.R")
	biocLite("org.Hs.eg.db")
	biocLite(c("GenomicFeatures", "AnnotationDbi"))
	library("org.Hs.eg.db")
	library("AnnotationDbi")
	library("GenomicFeatures")
	# all the possible mappings
	ls("package:org.Hs.eg.db")
	# convert Entrez_ids to gene_symbols
	myEntrez_ids <- c("1","10","100","1000","37690")
	mySymbols<- mget(myEntrez_ids, org.Hs.egSYMBOL, ifnotfound=NA)
	mySymbols
	unlist(mySymbols)
	# convert gene_symbols to Entrez_ids
	mySymbols_2 <- c("VEGFA","CTCF", "SNAI1","KDM1A")
	myEntrez_ids_2<- mget(mySymbols_2, org.Hs.egSYMBOL2EG, ifnotfound=NA)
	unlist(myEntrez_ids_2)
	?AnnotationDbi::mget # get help
	# or use the select function
	?AnnotationDbi::select
	head(keys(org.Hs.eg.db))
	keytypes(org.Hs.eg.db)
	select(org.Hs.eg.db, keys = mySymbols_2, columns=c("SYMBOL","REFSEQ","GENENAME","ENTREZID"),keytype="SYMBOL")
	select(org.Hs.eg.db, keys = myEntrez_ids, columns=c("SYMBOL","REFSEQ","GENENAME","ENTREZID"),keytype="ENTREZID")
	# How many gene symbols
	symbol <- keys(org.Hs.eg.db, "SYMBOL")
	length(symbol)
	############### use biomart ###################
	library(biomaRt)
	mart<- useMart(biomart = 'ensembl', dataset = 'hsapiens_gene_ensembl')
	# get sequences
	seq <- getSequence(id = 'BRCA1', type='hgnc_symbol',seqType="3utr", mart = mart) # pretty slow...
	show(seq)
	seq2 <-getSequence(id="ENST00000520540",type='ensembl_transcript_id',seqType='gene_flank', upstream =30, mart=mart)
	show(seq2)
	# convert gene ids gene symbol to refseq
	geneList<- c("VEGFA","CTCF", "SNAI1","KDM1A")
	results<- getBM(attributes = c("refseq_mrna","hgnc_symbol"), filters="hgnc_symbol", values=geneList, mart=mart)
	results
	?getBM

view raw convert_ids.r hosted with ❤ by GitHub

For more examples see posts from Dave Tang:
http://davetang.org/muse/2013/12/16/bioconductor-annotation-packages/
http://davetang.org/muse/2013/05/23/using-the-bioconductor-annotation-packages/
http://davetang.org/muse/2013/11/25/thoughts-converting-gene-identifiers/