refGenome (version 1.7.7)

refJunctions-class: Class "refJunctions"

Description

refJunctions represents ensembl genomic annotation data for splice-junctions.

Objects from the Class

Objects can be created by calls of the form getSpliceTable(rg) where 'rg' is an object of class refGenome (ensemblGenome or ucscGenome).

Slots

basedir:

Object of class "character" Directory where SQLite database is written.

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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.

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Methods

show

Creates a sensible printout.

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unifyJuncs

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.

%

getGenePositions

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.)

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Details

The getSpliceTable function eventually contains a "transcript_biotype" column (present in Ensembl genome). This coulumn is used by the "unifyJuncs"- method.

References

http://www.ensembl.org/info/data/ftp/index.html http://mblab.wustl.edu/GTF22.html#fields

Examples

# NOT RUN {
##-------------------------------------##
## A) Ensembl
##-------------------------------------##
ef <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ef)
enj <- getSpliceTable(ens)
ufe <- unifyJuncs(enj)
# }
# NOT RUN {
saveGenome(enj,"enj.RData", useBasedir=FALSE)
enjr <- loadGenome("enj.RData")
# }
# NOT RUN {
##-------------------------------------##
## B) UCSC
##-------------------------------------##
uf <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
uc <- loadGenome(uf)
ucj <- getSpliceTable(uc)
ufu <- unifyJuncs(ucj)
# }
# NOT RUN {
saveGenome(ucj, "ucj.RData",useBasedir=FALSE)
ucjr <- loadGenome("ucj.RData")
# }