| refGenome-package {refGenome} | R Documentation |
The package contains classes for managing (GTF-) annotation data for UCSC and Ensembl genomes. Data can be imported, merged, viewed, searched and saved (as .RData and as SQLite database). There is also a C-routine for detection of overlapping (alignment) ranges with annotated regions.
| Package: | refGenome |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2012-10-06 |
| License: | What license is it under? |
| Depends: | methods |
Wolfgang Kaisers Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
ens<-ensemblGenome()
basedir(ens) <- system.file("extdata",package="refGenome")
ens_gtf <- "hs.ensembl.62.small.gtf"
read.gtf(ens,ens_gtf)
ddx <- extractByGeneName(ens,"DDX11L1")
ddx
fam <- extractTranscript(ens,"ENST00000417324")
fam
enpa <- extractSeqids(ens,ensPrimAssembly())
enpa
tableTranscript.id(ens)
tableTranscript.name(ens)