Genomicrangesexample

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This is is an example of using Genomic Ranges and Genomic Features to match transcript ID's produced with cufflinks to transcript ID's from other sources.

Table of Contents Make Transcript Databases UCSC Ref Gene Ensembl from BioMart Cufflinks Extract Names from Transcript Databases Ref Gene Ensembl Cufflinks

Make Transcript Databases

First define a few things.

chromRename is required because the ensembl transcript database from bioMart uses, for example, "1" instead of "chr1"

newSeqLevelsToKeep and oldSeqLevelsToKeep are used to limit the chromosomes saved in the transcript databases.

UCSC Ref Gene

rn5RefGeneUCSC <- makeTranscriptDbFromUCSC(genome="rn5",tablename="refGene")
refGeneExonsByTranscript <- exonsBy(rn5RefGeneUCSC,by = "tx")
refGeneExonsByTranscript <- keepSeqlevels(refGeneExonsByTranscript,newSeqLevelsToKeep)

Ensembl from BioMart

bioMartEnsemblRn5 <- makeTranscriptDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL", dataset='rnorvegicus_gene_ensembl', host="uswest.ensembl.org")
bioMartExonsByTranscript <- exonsBy(bioMartEnsemblRn5,by="tx")
bioMartExonsByTranscript <- keepSeqlevels(bioMartExonsByTranscript,oldSeqLevelsToKeep)
bioMartExonsByTranscript <- renameSeqlevels(bioMartExonsByTranscript,chromRename)

Cufflinks

cuffToDB

This part uses the R program cuffToDB.R. The cufflinks file is a gtf file called combined.polyA.17Jan13.gtf.

source('cuffToDB.R')
gtfFile <- 'combined.polyA.17Jan13.gtf'
cuffLinksTxdb <- cuff2db(gtfFile)
cufflinksExonsByTranscript <- exonsBy(cuffLinksTxdb,by="tx")

Extract Names from Transcript Databases

Ref Gene

refGeneTranscript_IDs <- names(refGeneExonsByTranscript)
refGeneTranscriptNames <- select(rn5RefGeneUCSC,keys=refGeneTranscript_IDs, cols="TXNAME",keytype="TXID")

Ensembl

ensemblTranscript_IDs <- names(bioMartExonsByTranscript)
ensemblTranscriptNames <- select(bioMartEnsemblRn5,keys=ensemblTranscript_IDs, cols="TXNAME",keytype="TXID")

Cufflinks

cufflinksTranscript_IDs <- names(cufflinksExonsByTranscript)
cufflinksTranscriptNames <- select(cuffLinksTxdb,keys=cufflinksTranscript_IDs, cols="TXNAME",keytype="TXID")