R: Class '"refJunctions"'

refJunctions-class {refGenome} | R Documentation

## Class `"refJunctions"`

### Description

refJunctions represents ensembl genomic annotation data for splice-junctions.

### Details

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

### 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.

`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.

### Methods

show

  Creates a sensible printout.

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.)

### Author(s)

Wolfgang Kaisers

### References

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

### Examples

    ##-------------------------------------##
    ## 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")

[Package refGenome version 1.7.7 Index]