Description Objects from the Class Slots Methods Author(s) References Examples
refExons represents genomic annotation data on exon-features for Ensembl and UCSC genomes. Relative locations of CDS, start_codon and stop_codon features are added. The unifiedExons class is intended to be used as preparation of exonic coordinates for counting of alignments (reads) inside these regions. In order to prevent ambiguities, overlaps are removed.
Objects can be created by calls of the form refExons(rg)
.
'rg' represents an object of class ensemblGenome
or ucscGenome
.
basedir
:Object of class "character"
Directory
where SQLite database is written.
ev
:Object of class "environment"
Environment that contains data structures.
Optionally, there are gtf and attr data.frames.
signature(object = "ensemblExons")
:
Creates a sensible printout.
signature(object = "ensemblExons",
coding="logical")
:
Returns tabled splice sites.
When coding
=TRUE only entries with
gene_biotype=="protein_coding"
are included.
Wolfgang Kaisers
http://www.ensembl.org/info/data/ftp/index.html
http://mblab.wustl.edu/GTF22.html#fields
http://genome.ucsc.edu/
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ##-------------------------------------##
## A) Ensembl
##-------------------------------------##
ensfile <- system.file("extdata",
"hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ensfile)
enex <- refExons(ens)
saveGenome(enex,"enex.RData", useBasedir=FALSE)
er <- loadGenome("enex.RData")
# Unify exons
uex <- unifyRanges(enex)
##-------------------------------------##
## B) UCSC
##-------------------------------------##
ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
uc <- loadGenome(ucfile)
ucex <- refExons(uc)
saveGenome(ucex, "ucex.RData", useBasedir=FALSE)
ur <- loadGenome("ucex.RData")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.