Description Details Objects from the Class Slots Methods Author(s) References Examples
refJunctions represents ensembl genomic annotation data for splice-junctions.
The getSpliceTable function eventually contains a "transcript_biotype" column (present in Ensembl genome). This coulumn is used by the "unifyJuncs"- method.
Objects can be created by calls of the form getSpliceTable(rg) where 'rg' is
an object of class refGenome
(ensemblGenome or ucscGenome).
basedir
:Object of class "character"
Directory where SQLite database is written.
ev
:Object of class "environment"
Environment that contains data structures.
The splice-junction data is stored in 'gtf' named data.frame inside ev.
Optionally the environment also contains the result tables from
unifyJuncs
or getGenePositions
functions.
They are automatically included in save and load procedures.
Creates a sensible printout.
signature(object = "refJunctions")
:
Calculates unique splice-sites and associates each site with gene-id.
Adds uid to 'gtf' table and creates a new 'unique junction site'
(ujs) table.
signature(object="refJunctions",
force="logical")
:
Extracts table with position data for whole genes (smallest exon
start position and largest exon end position.
A copy of the table will be placed inside the internal environment.
Upon subsequent call only a copy of the contained table is returned
unless force=TRUE
is given.
Upon force=TRUE
new gene positions are calculated regardless
of existing tables.)
Wolfgang Kaisers
http://www.ensembl.org/info/data/ftp/index.html http://mblab.wustl.edu/GTF22.html#fields
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ##-------------------------------------##
## A) Ensembl
##-------------------------------------##
ef <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ef)
enj <- getSpliceTable(ens)
ufe <- unifyJuncs(enj)
saveGenome(enj,"enj.RData", useBasedir=FALSE)
enjr <- loadGenome("enj.RData")
##-------------------------------------##
## B) UCSC
##-------------------------------------##
uf <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
uc <- loadGenome(uf)
ucj <- getSpliceTable(uc)
ufu <- unifyJuncs(ucj)
saveGenome(ucj, "ucj.RData",useBasedir=FALSE)
ucjr <- loadGenome("ucj.RData")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.