refGenome (version 1.7.7)

refGenome-package: Managing annotation data for reference Genomes from UCSC and Ensembl.

Description

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.

Details

Package:	refGenome
Type:	Package
Version:	1.0
Date:	2012-10-06
License:	What license is it under?
Depends:	methods

Examples

# NOT RUN {
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)
# }