R: Managing annotation data for reference Genomes from UCSC and...

refGenome-package {refGenome} | R Documentation

## 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

### Author(s)

Wolfgang Kaisers Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>

### Examples

    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)

[Package refGenome version 1.7.7 Index]